Bowtie seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.9/samtools' Reference genome folder provided is /gscratch/srlab/sam/data/C_gigas/genomes/ (absolute path is '/gscratch/srlab/sam/data/C_gigas/genomes/)' Processing sequences up to read no. 10000000 from the input file Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Input files to be analysed (in current folder '/gscratch/scrubbed/samwhite/outputs/20190222_cgigas_pe_bismark/subset_10000000'): /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R1.fastq.gz /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R2.fastq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Setting parallelization to single-threaded (default) Current working directory is: /gscratch/scrubbed/samwhite/outputs/20190222_cgigas_pe_bismark/subset_10000000 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sam/data/C_gigas/genomes/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R1.fastq.gz and /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R2.fastq.gz Input files are in FastQ format Processing reads up to sequence no. 10000000 from /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R1.fastq.gz Writing a C -> T converted version of the input file cgig_bsseq_pe_all_R1.fastq.gz to cgig_bsseq_pe_all_R1.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file cgig_bsseq_pe_all_R1.fastq.gz (10000001 sequences in total) Processing reads up to sequence no. 10000000 from /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R2.fastq.gz Writing a G -> A converted version of the input file cgig_bsseq_pe_all_R2.fastq.gz to cgig_bsseq_pe_all_R2.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file cgig_bsseq_pe_all_R2.fastq.gz (10000001 sequences in total) Input files are cgig_bsseq_pe_all_R1.fastq.gz_C_to_T.fastq and cgig_bsseq_pe_all_R2.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sam/data/C_gigas/genomes/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from cgig_bsseq_pe_all_R1.fastq.gz_C_to_T.fastq and cgig_bsseq_pe_all_R2.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: HWI-ST700693:385:C3ATLACXX:4:1101:1831:2096/1 99 scaffold750_CT_converted 577176 1 36M = 577200 60 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG CC@FDFFFHHGHHJFBGIIJJIJEHGIJIJJJJJJG AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:36 YS:i:0 YT:Z:CP HWI-ST700693:385:C3ATLACXX:4:1101:1831:2096/2 147 scaffold750_CT_converted 577200 1 36M = 577176 -60 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGAGAG GJJJIJJJJJJJJJJJJJJJJJJHHHHHD;FFFCC@ AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:36 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from cgig_bsseq_pe_all_R1.fastq.gz_C_to_T.fastq and cgig_bsseq_pe_all_R2.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: HWI-ST700693:385:C3ATLACXX:4:1101:1831:2096/1 83 scaffold393_GA_converted 143720 1 36M = 143706 -50 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT GJJJJJJIJIGHEJIJJIIGBFJHHGHHFFFDF@CC AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:36 YS:i:0 YT:Z:CP HWI-ST700693:385:C3ATLACXX:4:1101:1831:2096/2 163 scaffold393_GA_converted 143706 1 36M = 143720 50 CTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCT @CCFFF;DHHHHHJJJJJJJJJJJJJJJJJJIJJJG AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:36 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to cgig_bsseq_pe_all_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R1.fastq.gz and /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R2.fastq.gz Chromosomal sequence could not be extracted for HWI-ST700693:385:C3ATLACXX:4:1101:5142:25699 C24196 1 Chromosomal sequence could not be extracted for HWI-ST700693:385:C3ATLACXX:4:1105:4856:63835 C22548 1 Chromosomal sequence could not be extracted for HWI-ST700693:385:C3ATLACXX:4:1110:1457:54826 scaffold43686 300769 Chromosomal sequence could not be extracted for HWI-ST700693:385:C3ATLACXX:4:1110:4272:93059 C21764 1511 Chromosomal sequence could not be extracted for HWI-ST700693:385:C3ATLACXX:4:1116:2368:7379 scaffold38090 52535 Chromosomal sequence could not be extracted for HWI-ST700693:385:C3ATLACXX:4:1202:5993:5262 scaffold32624 12059 Chromosomal sequence could not be extracted for HWI-ST700693:385:C3ATLACXX:4:1311:4068:17280 scaffold31954 10506 Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-ST700693:385:C3ATLACXX:4:2110:7883:8526 scaffold820 12177 Chromosomal sequence could not be extracted for HWI-ST700693:385:C3ATLACXX:4:2115:13896:21944 C29202 6296 Chromosomal sequence could not be extracted for HWI-ST700693:385:C3ATLACXX:4:2115:14740:74866 scaffold968 1 Chromosomal sequence could not be extracted for HWI-ST700693:385:C3ATLACXX:4:2210:10409:80281 C24562 2765 Chromosomal sequence could not be extracted for HWI-ST700693:385:C3ATLACXX:4:2302:18111:87639 scaffold1543 75281 Chromosomal sequence could not be extracted for HWI-ST700693:385:C3ATLACXX:4:2304:13025:52866 scaffold514 545590 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1108:3243:64899 C24850 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1116:18282:33267 scaffold422 571151 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1212:4119:92664 C22844 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1309:13364:61734 scaffold40002 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1314:13488:58831 C29914 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2111:1902:90967 C16312 1 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2115:12466:35880 C19632 793 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2202:13231:64191 C30946 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2211:17251:49236 C31982 10534 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2305:9793:51855 C13670 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2307:13437:94978 C16318 296 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2308:17999:76027 C22114 1649 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2312:2217:17764 scaffold37906 49307 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2316:8125:61582 scaffold43708 307072 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1104:15396:85261 C23682 2315 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1109:10564:43163 scaffold40526 93686 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1111:5051:9548 scaffold36778 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1202:10373:14932 C29882 7083 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1301:6790:53328 C15378 225 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1307:3458:12677 scaffold26300 3768 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1307:7978:77375 C26010 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1308:13296:94127 scaffold931 3 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1314:3710:37333 scaffold90 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1315:6452:93474 scaffold920 665 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2107:6635:92485 scaffold33428 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2111:16518:47570 scaffold34032 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2112:4733:11201 scaffold546 671116 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2114:3911:78328 C26198 3711 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2116:6375:73457 C19902 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2208:20853:68622 C28408 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2308:14277:82004 C19356 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2308:11707:84503 C23868 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2309:2663:87373 scaffold1220 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2313:18611:77086 scaffold34894 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2316:2615:18288 C27276 4482 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1102:4511:90431 C20550 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1104:13520:60250 C33332 13890 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1105:4960:61551 C21312 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1105:18091:97546 C14780 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1106:17676:39873 C34436 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1108:18717:6257 C26570 3969 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1109:19378:41363 C23682 2306 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1109:5793:59367 C19406 748 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1110:11367:80644 scaffold352 319595 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1111:9395:30477 scaffold715 156505 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1111:1586:64754 scaffold24412 2614 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1111:14221:82192 scaffold641 4064 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1112:14836:100573 scaffold38360 55240 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1113:14347:96274 C26690 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1115:13495:13495 C33182 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1116:19232:72690 C13344 149 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1201:16527:86659 C28184 5253 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1202:15308:59676 scaffold36314 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1203:3534:33827 C32328 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1203:7944:66249 C31714 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1203:15395:77863 scaffold716 401243 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1208:12408:74143 C25056 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1209:15877:27476 scaffold38908 63646 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1209:10164:38200 C19984 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1209:7797:66314 scaffold514 545550 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1209:15884:69342 C15630 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1210:17417:13163 C32578 11932 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1210:4886:49407 scaffold40526 93683 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1210:13953:75261 C22800 1908 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1212:12431:25421 scaffold1085 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1216:3941:29249 C23868 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1216:16197:97521 scaffold38756 2 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1307:9592:12311 C28340 5399 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1308:15516:23525 C19252 711 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1313:7436:69713 scaffold221 207814 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1313:9714:77612 C21312 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1314:13724:42028 C27928 5014 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1314:2088:72584 scaffold30 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1316:2908:34542 C30766 8266 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1316:12069:89512 scaffold1001 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2104:15153:77817 scaffold1218 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2106:16911:53664 C21726 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2107:2485:75708 C23024 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2109:3985:63813 C26570 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2109:6989:91975 scaffold1223 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2110:9523:78213 scaffold251 122291 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2110:7379:99442 scaffold37 261120 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2111:9774:29909 C30946 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2111:12370:62819 C19354 739 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2111:5312:88326 scaffold34534 19391 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2113:10153:76819 C24320 2605 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2114:7979:89608 C23264 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2115:20981:59227 scaffold1354 417413 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2115:12738:93240 C20728 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2116:15974:9932 scaffold38274 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2116:8237:14099 C15086 212 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2206:7524:16301 scaffold18778 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2209:17741:92187 scaffold680 70132 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2209:2271:96455 scaffold36630 36587 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2212:20636:44893 scaffold44 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2214:7229:67817 C31714 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2215:15786:84949 C24524 2711 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2305:11956:23372 scaffold365 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2308:9970:70146 C34176 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2308:12585:97652 C30434 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2310:5439:93452 scaffold30010 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2311:2721:15005 scaffold1726 437309 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2311:1661:43781 C24640 2773 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2312:12959:12687 C33128 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2312:12075:38838 C17244 396 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2312:13884:60192 scaffold793 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2313:16822:44879 C13242 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2314:2279:54502 C29322 6403 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2314:10595:78018 C29006 2 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:2315:14181:28888 scaffold1433 1255 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1101:8864:52220 scaffold32252 11030 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1101:8641:66384 C17922 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1102:9671:25782 C16402 311 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1102:19025:69843 C33666 14997 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1103:14071:17161 C29992 7209 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1103:19817:55984 C20856 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1103:14795:66871 C27712 4828 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1104:8619:15833 scaffold208 247942 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1104:7511:88472 C28070 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1104:6910:89443 scaffold41898 137745 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1104:13129:96402 scaffold1470 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1105:16685:12125 scaffold25284 3085 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1105:10387:20850 C34176 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1105:14877:28724 scaffold1868 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1105:11436:28955 scaffold37990 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1105:18030:42317 scaffold344 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1105:7395:85920 scaffold451 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1106:2237:4464 C24814 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1106:2201:36372 scaffold40194 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1106:3828:75719 scaffold43084 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1106:16205:80479 C24232 2564 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1107:4096:23805 C32438 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1107:2461:27760 C13046 133 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1107:13386:31985 C24688 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1107:16315:52756 scaffold31320 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1107:20668:85116 C15156 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1108:12606:44182 scaffold38354 54689 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1108:11978:68572 C15352 230 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1108:3862:73789 scaffold24 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1109:17333:4147 scaffold39368 69005 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1109:8073:6385 scaffold1261 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1109:11368:41024 C32994 12988 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1110:1876:11962 scaffold36936 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1111:12589:78270 scaffold607 805 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1113:8795:13082 C19576 779 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1113:5862:22594 scaffold43608 3 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1113:9959:30021 C34634 19666 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1113:20362:86184 C19838 833 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1113:3425:94171 scaffold579 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1114:7425:2747 scaffold34956 21421 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1114:12122:48110 C24204 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1114:13931:48573 C30946 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1114:5981:51824 scaffold33066 13114 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1114:17357:54570 C24964 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1114:10628:67478 scaffold37558 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1114:16303:84513 C29992 7209 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1114:16957:94805 C32108 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1114:14368:98032 C34712 20063 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1115:18175:13608 scaffold1376 3 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1115:11752:24492 scaffold157 679231 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1115:1472:53479 scaffold33518 14456 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1115:18292:77959 scaffold451 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1115:2993:84648 scaffold31792 10145 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1116:4352:20180 C23490 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1116:7310:20878 scaffold41828 133120 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1116:12811:25674 C16738 337 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1116:16304:48154 scaffold39732 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1116:3592:61332 C25546 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1116:13457:78936 scaffold318 2186 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1201:4711:12749 C31572 1 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1202:6777:27019 C26102 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1203:12020:61582 scaffold715 156501 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1203:8846:83050 C24616 2756 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1204:17812:42344 C32842 12646 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1204:7888:43243 scaffold40156 85251 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1204:6473:61891 C30324 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1205:14902:36204 scaffold42364 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1205:5520:49386 scaffold37966 46329 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1205:3426:68615 C33126 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1205:11550:80505 scaffold330 4729 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1205:18734:87948 scaffold39744 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1206:13270:53094 C23360 2144 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1206:17650:75737 C15600 246 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1206:3013:76039 scaffold34894 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1206:20281:79871 C23436 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1206:17588:84516 C19902 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1207:9861:23400 C22958 1956 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1207:9598:29613 C21818 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1207:8246:33238 scaffold38222 53499 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1208:20474:6683 scaffold999 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1208:4660:21134 C25394 3187 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1209:20868:11813 C13274 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1209:20114:29068 C31202 8943 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1209:9158:29454 C16780 347 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1209:3506:47876 scaffold30230 3 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1209:8634:67902 C33332 13890 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1209:21015:75199 scaffold85 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1210:16958:17862 C31996 10554 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1210:10275:27426 C15436 228 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1210:15770:34263 C22722 1881 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1210:16513:76064 scaffold38 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1211:3693:17777 C27526 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1211:4978:18698 C29408 6511 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1211:10002:78975 C30046 3 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1211:2425:90540 C27746 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1211:14565:93169 C20550 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1212:4272:11574 scaffold42892 199807 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1212:14710:25808 C31828 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1212:6682:52146 scaffold384 3217 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1212:14427:97146 scaffold1282 85676 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1213:9569:31094 scaffold38700 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1213:20332:52739 scaffold41970 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1213:5352:83988 scaffold413 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1214:6635:4374 scaffold37790 48113 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1214:2448:28157 C14548 190 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1214:18806:66243 C22870 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1214:10984:74318 C24530 2709 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1215:16597:11474 scaffold35366 24173 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1215:19090:12934 C29294 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1215:2411:42239 scaffold36808 38066 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1215:3882:49730 scaffold935 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1215:6339:52804 scaffold36020 29985 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1215:10469:72280 C32260 11114 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1216:4631:25312 scaffold40420 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1216:1611:35991 scaffold1879 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1216:15646:37811 C30496 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1301:18745:12271 scaffold1589 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1301:1969:37295 scaffold616 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1301:16087:62185 C22422 1766 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1302:5051:46402 C14468 184 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1302:6833:81628 scaffold43842 2 Processed 6000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1304:12604:8462 C30046 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1304:6307:51511 scaffold186 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1304:14578:81681 scaffold1817 122659 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1304:15443:84634 scaffold772 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1304:2213:97612 scaffold34420 18731 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1305:12155:29496 C17966 487 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1306:14615:52100 C21700 1455 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1306:13858:97832 C23162 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1307:10149:11960 scaffold1899 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1307:18395:71367 C19848 837 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1308:8021:61202 scaffold19 276236 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1308:10466:70988 C19902 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1308:9649:75060 scaffold40038 82674 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1309:8400:31850 scaffold1374 73172 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1309:13307:37911 C23868 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1309:17650:42035 C18448 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1309:5672:54654 C23160 2051 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1309:20323:76996 scaffold84 803 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1310:18105:18090 C21850 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1310:19387:54348 scaffold1584 420517 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1310:9131:55467 C13868 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1310:4981:93204 C24346 2616 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1311:19319:18894 C28408 5459 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1311:17905:32441 scaffold1853 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1311:9885:56375 scaffold37668 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1312:13855:79158 C12924 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1312:15946:80614 C14554 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1313:3578:5844 scaffold37 261120 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1313:9076:58223 scaffold34894 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1313:7083:78665 C19246 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1313:10415:88637 scaffold41082 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1313:15027:89349 C30956 8552 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1314:21000:6304 scaffold22038 1553 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1314:7688:20591 C16340 297 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1314:9984:51778 C33332 13890 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1314:20350:58892 C25394 3190 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1314:5664:71651 C19902 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1315:2356:6931 C28628 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1315:13914:39611 scaffold39184 67077 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1315:12617:64519 scaffold30 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1315:3952:93395 scaffold1504 4030 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1315:11782:95927 scaffold39740 76540 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1316:1615:14797 C15554 241 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:1316:10524:99192 C30398 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2101:10675:25173 scaffold1803 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2101:12891:47132 C19902 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2101:13327:68196 scaffold37622 46215 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2101:9333:87220 C15788 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2102:11173:26994 scaffold20312 913 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2102:10029:78679 C19814 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2103:3740:19827 scaffold1238 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2103:10571:23870 C30988 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2103:5437:68028 scaffold18084 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2103:10379:68474 scaffold160 656123 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2103:8511:70069 C22318 2 Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2104:15993:8019 C12842 131 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2104:4618:11848 scaffold31748 10038 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2105:20893:39314 C13878 161 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2105:3057:84772 scaffold251 122294 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2106:13611:7405 C18074 502 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2106:8182:9426 scaffold39472 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2106:4331:36319 C15434 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2106:2712:39438 C17830 470 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2106:10957:60407 C29526 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2106:13538:92894 C25236 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2107:3685:13616 C22406 1757 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2107:3446:23186 scaffold40526 93685 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2107:14538:79322 C32028 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2107:14495:93449 C23804 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2107:13470:94623 C33332 13890 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2108:9518:7062 scaffold34534 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2108:2500:35915 scaffold41214 111970 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2108:7417:36855 C30426 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2108:3833:48742 C19902 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2109:19713:51638 C28990 6028 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2109:9131:61533 scaffold42528 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2110:18322:13030 scaffold251 122290 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2110:14074:63620 scaffold323 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2110:3450:74396 scaffold44 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2111:1543:6543 scaffold1470 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2111:12231:19571 scaffold43278 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2111:12799:20158 scaffold38672 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2111:12636:21389 scaffold37418 44031 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2111:8907:23638 scaffold1308 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2112:9451:49460 C25088 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2113:3754:6514 scaffold1641 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2113:5940:30512 C31828 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2113:5074:40370 scaffold42794 188835 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2113:2625:75988 scaffold1764 19658 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2114:15678:23555 C33332 13890 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2114:15961:25329 scaffold38700 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2114:12993:29143 C27478 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2114:8697:48158 scaffold1829 159244 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2114:9239:77537 C19672 797 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2114:16496:78309 scaffold32844 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2114:18386:96072 scaffold418 214571 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2115:3948:10188 scaffold1005 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2115:1753:20290 scaffold37668 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2115:20987:44533 C30496 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2115:2655:90891 scaffold695 831410 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2116:3192:48742 C15294 226 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2116:3368:82699 C34176 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2116:4504:86635 scaffold420 5897 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2116:17495:94947 C26674 4040 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2116:10774:99778 scaffold390 4036 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2202:11330:2239 C30956 8558 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2202:10576:13268 scaffold38492 56445 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2202:14892:22576 C27132 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2202:11232:23318 C23024 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2203:11617:17624 C27478 1 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2204:18856:48704 C16356 303 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2205:14060:55026 C28468 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2205:5808:78000 C23042 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2206:9502:18812 scaffold102 1727044 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2206:15890:23901 scaffold799 28545 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2206:16652:35983 scaffold1231 108579 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2206:15769:38234 C16318 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2206:4308:44887 C30870 8432 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2206:14454:55691 C15158 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2206:15136:67631 C27928 5019 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2206:1149:69859 C15322 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2207:15263:5554 C22092 1630 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2208:17863:15141 C22422 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2208:9958:64409 C31256 9069 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2208:15505:75856 scaffold6 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2208:18671:79052 C27284 4484 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2208:12271:86957 C23878 2391 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2209:16600:39981 scaffold26804 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2210:5920:20319 scaffold38704 59847 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2210:6573:58845 C31292 9155 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2210:7319:80057 C25954 3543 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2211:4645:75262 scaffold38194 53372 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2212:11073:8481 scaffold44006 433862 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2212:15125:41431 C23682 2308 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2212:8866:67993 scaffold37576 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2212:20941:70063 scaffold558 743 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2213:15808:11139 scaffold24772 2795 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2213:1686:29060 scaffold379 8416 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2213:20047:58978 scaffold37966 46329 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2213:11743:60042 scaffold33134 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2213:20410:63803 scaffold38996 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2213:1483:69219 C19984 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2213:15975:87040 scaffold1704 255049 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2213:4415:94309 scaffold1288 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2214:21146:40223 scaffold28972 5803 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2214:2478:77448 scaffold1764 19664 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2215:13755:28741 C14220 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2215:9551:30699 C26402 3833 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2215:20757:44724 C17386 410 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2215:4951:53457 scaffold300 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2216:15977:40056 C28454 5497 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2216:9296:49750 C24346 2624 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2216:2388:91012 C24910 2908 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2301:19102:49529 scaffold339 217889 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2301:3042:65735 scaffold18084 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2302:13079:67155 scaffold34894 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2302:20676:71881 C30686 8163 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2302:3178:87538 C23866 2386 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2302:13624:88916 C19576 784 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2303:5569:4080 C26992 4248 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2303:4782:6067 C22844 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2303:16391:78299 C25698 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2304:1819:22154 scaffold38492 56445 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2304:1628:44524 C23428 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2304:2753:54803 scaffold37740 2 Processed 9000000 sequence pairs so far Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2304:19022:69833 C32438 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2304:14883:91797 scaffold42144 148296 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2305:8832:19746 C16736 337 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2305:18889:44086 C16318 295 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2306:8891:23270 C27386 4574 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2306:1670:32949 scaffold1772 412134 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2306:10674:69337 C26986 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2306:18729:95996 C14436 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2307:3119:53514 C29294 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2307:16413:61044 C32224 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2307:1306:74369 scaffold44064 481413 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2307:1289:74393 scaffold44064 481413 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2307:14932:76790 C33332 13890 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2307:20776:96578 scaffold33628 14778 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2308:5914:74818 scaffold43608 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2309:9833:67505 C22662 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2310:15412:14617 C32424 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2310:4528:18279 C19902 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2310:8106:45910 C23878 2393 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2310:18230:45853 scaffold100 1174919 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2310:4227:51426 C17320 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2310:14925:58599 scaffold43494 3 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2310:13787:78663 C30728 8212 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2310:16738:82833 C14944 201 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2310:1940:85892 C16318 294 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2310:16574:97863 C15160 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2311:12371:23449 C17688 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2311:2439:83039 C30946 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2312:12966:4894 scaffold18830 590 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2312:6156:55047 scaffold818 402405 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2312:18545:79933 C26454 3874 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2312:20060:97314 C20856 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2313:11647:32026 C15520 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2313:7495:66581 C27210 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2314:11661:3717 C19814 3 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2315:18662:22327 C19104 676 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2315:18036:27441 C23868 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2315:17238:49587 C24320 2605 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2316:6120:19895 C30336 1 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2316:6005:27795 scaffold728 2 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2316:8967:36005 scaffold1616 224339 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2316:6793:51924 C14468 178 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2316:14785:74972 scaffold38996 64176 Chromosomal sequence could not be extracted for HWI-ST700693:351:D2CA8ACXX:7:2316:18114:77740 scaffold621 517882 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1101:12439:19105 scaffold972 1 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1102:11937:38396 scaffold625 840115 Chromosomal sequence could not be extracted for HWI-ST700693:373:C39EMACXX:4:1103:17390:60283 C18442 539 10000000 reads; of these: 10000000 (100.00%) were paired; of these: 6181452 (61.81%) aligned concordantly 0 times 2138464 (21.38%) aligned concordantly exactly 1 time 1680084 (16.80%) aligned concordantly >1 times 38.19% overall alignment rate 10000000 reads; of these: 10000000 (100.00%) were paired; of these: 6172062 (61.72%) aligned concordantly 0 times 2145218 (21.45%) aligned concordantly exactly 1 time 1682720 (16.83%) aligned concordantly >1 times 38.28% overall alignment rate Processed 10000000 sequence pairs so far Processed 10000000 sequences in total Successfully deleted the temporary files cgig_bsseq_pe_all_R1.fastq.gz_C_to_T.fastq and cgig_bsseq_pe_all_R2.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 10000000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 105307378 Total methylated C's in CpG context: 1947531 Total methylated C's in CHG context: 44570 Total methylated C's in CHH context: 155977 Total methylated C's in Unknown context: 10465 Total unmethylated C's in CpG context: 10236643 Total unmethylated C's in CHG context: 17172924 Total unmethylated C's in CHH context: 75749733 Total unmethylated C's in Unknown context: 206032 C methylated in CpG context: 16.0% C methylated in CHG context: 0.3% C methylated in CHH context: 0.2% C methylated in unknown context (CN or CHN): 4.8% Bismark completed in 0d 1h 37m 9s ==================== Bismark run complete ====================