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/O_lurida/genomes/Olurida_v081/oly_v081_bismark_genome/ (absolute path is '/gscratch/srlab/sam/data/O_lurida/genomes/Olurida_v081/oly_v081_bismark_genome/)' Processing sequences up to read no. 1000000 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/20190224_olurida_se_bismark/subset_1000000'): /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/olur_bsseq_all_R1.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/20190224_olurida_se_bismark/subset_1000000 Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sam/data/O_lurida/genomes/Olurida_v081/oly_v081_bismark_genome/ Single-core mode: setting pid to 1 Single-end alignments will be performed ======================================= Input file is in FastQ format Processing reads up to sequence no. 1000000 from /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/olur_bsseq_all_R1.fastq.gz Writing a C -> T converted version of the input file olur_bsseq_all_R1.fastq.gz to olur_bsseq_all_R1.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file olur_bsseq_all_R1.fastq.gz (1000001 sequences in total) Input file is olur_bsseq_all_R1.fastq.gz_C_to_T.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sam/data/O_lurida/genomes/Olurida_v081/oly_v081_bismark_genome/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from olur_bsseq_all_R1.fastq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --norc) Using Bowtie 2 index: /gscratch/srlab/sam/data/O_lurida/genomes/Olurida_v081/oly_v081_bismark_genome/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: HWI-D00743:54:C8MOMACXX:1:1101:1413:2213_1:N:0:GGCTAC 0 Contig68945_CT_converted 3260 40 51M * 0 0 AGATGGATTTTTTTTGGAATAAATTTGATTGTTATTGTTTTTGATATTTTA CCCFFFFFHHHHHJJHJIIJIIIJJJJIJJJJJGIJIIIIJJIGIGIJJJI AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15A35 YT:Z:UU Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from olur_bsseq_all_R1.fastq.gz_C_to_T.fastq with options -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals --nofw) Using Bowtie 2 index: /gscratch/srlab/sam/data/O_lurida/genomes/Olurida_v081/oly_v081_bismark_genome/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: HWI-D00743:54:C8MOMACXX:1:1101:1413:2213_1:N:0:GGCTAC 4 * 0 0 * * 0 0 AGATGGATTTTTTTTGGAATAAATTTGATTGTTATTGTTTTTGATATTTTA CCCFFFFFHHHHHJJHJIIJIIIJJJJIJJJJJGIJIIIIJJIGIGIJJJI YT:Z:UU >>> Writing bisulfite mapping results to olur_bsseq_all_R1_bismark_bt2.bam <<< Reading in the sequence file /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/olur_bsseq_all_R1.fastq.gz Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:4347:2281_1:N:0:GGCTAC Contig150331 1132 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:5376:3134_1:N:0:GGCTAC Contig91563 4015 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:17166:4061_1:N:0:GGCTAC Contig137622 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:5908:8127_1:N:0:GGCTAC Contig62700 12542 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:15584:10948_1:N:0:GGCTAC Contig136606 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:20895:11557_1:N:0:GGCTAC Contig61059 13263 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:16834:12905_1:N:0:GGCTAC Contig103061 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:13764:15530_1:N:0:GGCTAC Contig58471 12756 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:5252:17437_1:N:0:GGCTAC Contig64696 1930 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:4688:18123_1:N:0:GGCTAC Contig58295 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:9031:21273_1:N:0:GGCTAC Contig81887 7685 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:11541:23175_1:N:0:GGCTAC Contig31194 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:4494:28672_1:N:0:GGCTAC Contig86549 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:1455:32979_1:N:0:GGCTAC Contig89321 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:13971:35149_1:N:0:GGCTAC Contig8342 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:20218:35803_1:N:0:GGCTAC Contig4243 4822 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:8283:36165_1:N:0:GGCTAC Contig91786 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:19453:43618_1:N:0:GGCTAC Contig73061 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:3706:48640_1:N:0:GGCTAC Contig61175 21107 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:11593:48655_1:N:0:GGCTAC Contig7889 4048 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:2939:50408_1:N:0:GGCTAC Contig85771 3766 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:6515:51728_1:N:0:GGCTAC Contig170236 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:18033:53654_1:N:0:GGCTAC Contig155853 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:4646:54966_1:N:0:GGCTAC Contig95638 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:4910:55470_1:N:0:GGCTAC Contig273050 2048 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:18569:55548_1:N:0:GGCTAC Contig151615 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:1532:60430_1:N:0:GGCTAC Contig198517 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:3845:61407_1:N:0:GGCTAC Contig140986 5961 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:18023:64092_1:N:0:GGCTAC Contig136884 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:17964:68817_1:N:0:GGCTAC Contig147984 3646 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:7470:74674_1:N:0:GGCTAC Contig73164 4170 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:13391:83918_1:N:0:GGCTAC Contig50092 14727 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:12498:85448_1:N:0:GGCTAC Contig77238 1311 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1101:8953:94533_1:N:0:GGCTAC Contig68181 2475 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:15772:4429_1:N:0:GGCTAC Contig97752 7990 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:3321:4677_1:N:0:GGCTAC Contig114458 2272 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:6273:7840_1:N:0:GGCTAC Contig123727 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:21017:7890_1:N:0:GGCTAC Contig33816 21218 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:5176:8223_1:N:0:GGCTAC Contig556401 1014 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:12079:12646_1:N:0:GGCTAC Contig77554 4667 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:17607:14045_1:N:0:GGCTAC Contig81818 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:1819:17979_1:N:0:GGCTAC Contig114505 4631 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:5847:20131_1:N:0:GGCTAC Contig149964 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:12424:23388_1:N:0:GGCTAC Contig46164 2603 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:5841:25217_1:N:0:GGCTAC Contig127394 5030 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:2570:25922_1:N:0:GGCTAC Contig24992 2193 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:3167:35049_1:N:0:GGCTAC Contig111992 1806 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:2648:36615_1:N:0:GGCTAC Contig121514 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:8099:37675_1:N:0:GGCTAC Contig194027 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:6216:38455_1:N:0:GGCTAC Contig107186 1310 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:19081:38525_1:N:0:GGCTAC Contig134324 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:18954:38781_1:N:0:GGCTAC Contig109433 4007 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:13755:39923_1:N:0:GGCTAC Contig68297 3711 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:8788:41696_1:N:0:GGCTAC Contig62739 10345 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:11430:44806_1:N:0:GGCTAC Contig8535 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:14607:45785_1:N:0:GGCTAC Contig126469 3513 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:6724:48048_1:N:0:GGCTAC Contig127062 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:14390:52873_1:N:0:GGCTAC Contig650 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:9078:53112_1:N:0:GGCTAC Contig46651 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:11107:53125_1:N:0:GGCTAC Contig198911 1122 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:16570:53767_1:N:0:GGCTAC Contig64786 25154 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:20708:54777_1:N:0:GGCTAC Contig101805 1365 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:5643:55915_1:N:0:GGCTAC Contig96536 3416 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:3997:61528_1:N:0:GGCTAC Contig91261 7142 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:6382:62705_1:N:0:GGCTAC Contig74658 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:13854:66869_1:N:0:GGCTAC Contig211510 1143 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:2343:72750_1:N:0:GGCTAC Contig16586 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:10448:73575_1:N:0:GGCTAC Contig1091 23957 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:6298:74422_1:N:0:GGCTAC Contig137459 985 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:9736:79930_1:N:0:GGCTAC Contig65230 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:15928:80672_1:N:0:GGCTAC Contig1994 17848 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:20752:85792_1:N:0:GGCTAC Contig418836 1074 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:10938:86965_1:N:0:GGCTAC Contig128222 1197 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:10527:87362_1:N:0:GGCTAC Contig23361 1427 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:18067:94594_1:N:0:GGCTAC Contig120994 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:2470:95310_1:N:0:GGCTAC Contig88172 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:5618:95600_1:N:0:GGCTAC Contig189411 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:10794:100257_1:N:0:GGCTAC Contig206446 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1102:15573:101022_1:N:0:GGCTAC Contig345869 1166 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:6036:5254_1:N:0:GGCTAC Contig193606 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:15817:6057_1:N:0:GGCTAC Contig30194 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:12364:9882_1:N:0:GGCTAC Contig98011 3408 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:1678:18353_1:N:0:GGCTAC Contig65230 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:17282:22648_1:N:0:GGCTAC Contig8057 8167 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:19746:22654_1:N:0:GGCTAC Contig111317 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:17334:23314_1:N:0:GGCTAC Contig7028 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:4673:25988_1:N:0:GGCTAC Contig213444 4112 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:18367:26160_1:N:0:GGCTAC Contig110263 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:19007:27419_1:N:0:GGCTAC Contig90762 3368 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:12801:30895_1:N:0:GGCTAC Contig16235 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:5112:35398_1:N:0:GGCTAC Contig85061 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:5890:36562_1:N:0:GGCTAC Contig67597 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:4934:37574_1:N:0:GGCTAC Contig95763 1374 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:14929:42044_1:N:0:GGCTAC Contig7930 3379 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:13418:42617_1:N:0:GGCTAC Contig49094 2904 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:15033:43782_1:N:0:GGCTAC Contig32939 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:15778:43874_1:N:0:GGCTAC Contig97652 5228 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:15760:46002_1:N:0:GGCTAC Contig204217 7743 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:18210:53520_1:N:0:GGCTAC Contig36106 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:11654:56663_1:N:0:GGCTAC Contig93947 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:1338:57142_1:N:0:GGCTAC Contig67 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:10331:57742_1:N:0:GGCTAC Contig64786 25155 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:17827:58655_1:N:0:GGCTAC Contig72382 12231 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:11735:62087_1:N:0:GGCTAC Contig39678 4941 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:13004:65617_1:N:0:GGCTAC Contig62375 9700 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:9833:65975_1:N:0:GGCTAC Contig103734 1366 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:14848:67897_1:N:0:GGCTAC Contig36582 4635 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:12965:70136_1:N:0:GGCTAC Contig157976 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:4308:73258_1:N:0:GGCTAC Contig50564 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:8499:74655_1:N:0:GGCTAC Contig413 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:16836:75844_1:N:0:GGCTAC Contig86765 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:18623:76961_1:N:0:GGCTAC Contig213835 1407 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:16022:77894_1:N:0:GGCTAC Contig66428 6742 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:10286:78382_1:N:0:GGCTAC Contig2813 17268 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:16386:79815_1:N:0:GGCTAC Contig38293 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:15793:82499_1:N:0:GGCTAC Contig32939 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:6237:83094_1:N:0:GGCTAC Contig75451 2622 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:8553:84252_1:N:0:GGCTAC Contig38333 26945 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:16694:86692_1:N:0:GGCTAC Contig147984 3647 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:21154:87123_1:N:0:GGCTAC Contig128854 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:2395:88314_1:N:0:GGCTAC Contig83012 3554 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:5759:90844_1:N:0:GGCTAC Contig51466 10978 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:9745:91779_1:N:0:GGCTAC Contig118742 3820 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:17758:92828_1:N:0:GGCTAC Contig70667 3887 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:14299:93925_1:N:0:GGCTAC Contig57650 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:4189:95750_1:N:0:GGCTAC Contig9137 6876 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1103:12447:100451_1:N:0:GGCTAC Contig208557 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:19544:4462_1:N:0:GGCTAC Contig179264 3782 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:17823:5999_1:N:0:GGCTAC Contig151615 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:1699:7087_1:N:0:GGCTAC Contig93675 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:14987:7899_1:N:0:GGCTAC Contig41004 31798 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:2483:10322_1:N:0:GGCTAC Contig148895 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:2901:16538_1:N:0:GGCTAC Contig171315 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:14181:16977_1:N:0:GGCTAC Contig16086 20557 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:8919:17339_1:N:0:GGCTAC Contig102373 1663 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:2941:17665_1:N:0:GGCTAC Contig127398 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:16281:18385_1:N:0:GGCTAC Contig290 36246 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:4149:19352_1:N:0:GGCTAC Contig84697 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:14371:25216_1:N:0:GGCTAC Contig17041 8271 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:15579:26480_1:N:0:GGCTAC Contig1349 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:17031:29505_1:N:0:GGCTAC Contig110389 1664 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:17720:29948_1:N:0:GGCTAC Contig206614 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:11833:30884_1:N:0:GGCTAC Contig52426 7827 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:10923:34077_1:N:0:GGCTAC Contig59187 1690 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:8581:39185_1:N:0:GGCTAC Contig90228 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:6831:39343_1:N:0:GGCTAC Contig166943 2342 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:9360:41827_1:N:0:GGCTAC Contig24480 2499 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:18914:42070_1:N:0:GGCTAC Contig107422 1855 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:18333:43149_1:N:0:GGCTAC Contig205100 10565 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:13885:58267_1:N:0:GGCTAC Contig196877 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:9090:69308_1:N:0:GGCTAC Contig31255 10100 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:12952:70101_1:N:0:GGCTAC Contig131711 9645 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:8168:72224_1:N:0:GGCTAC Contig118248 7930 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:7754:72865_1:N:0:GGCTAC Contig33842 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:12673:73821_1:N:0:GGCTAC Contig6585 5507 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:19238:75099_1:N:0:GGCTAC Contig131517 3002 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:19604:79031_1:N:0:GGCTAC Contig89262 1263 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:17542:80478_1:N:0:GGCTAC Contig6714 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:2563:81240_1:N:0:GGCTAC Contig48296 10890 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:4160:88033_1:N:0:GGCTAC Contig20637 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:6657:88109_1:N:0:GGCTAC Contig95655 2322 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:18923:89867_1:N:0:GGCTAC Contig86018 9276 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:14698:92671_1:N:0:GGCTAC Contig23469 11586 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:7283:93433_1:N:0:GGCTAC Contig133242 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:13707:93649_1:N:0:GGCTAC Contig45942 12254 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:9414:94760_1:N:0:GGCTAC Contig57641 5469 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1104:15313:98529_1:N:0:GGCTAC Contig188808 1269 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:1348:2547_1:N:0:GGCTAC Contig9137 6876 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:2877:2590_1:N:0:GGCTAC Contig39302 12483 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:10137:4390_1:N:0:GGCTAC Contig57162 11486 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:6676:4738_1:N:0:GGCTAC Contig157738 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:17436:6235_1:N:0:GGCTAC Contig41280 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:12454:7373_1:N:0:GGCTAC Contig207431 1743 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:18377:10351_1:N:0:GGCTAC Contig109879 2095 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:7533:11575_1:N:0:GGCTAC Contig73872 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:20490:13736_1:N:0:GGCTAC Contig28227 54605 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:18759:16576_1:N:0:GGCTAC Contig8057 8167 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:1652:21903_1:N:0:GGCTAC Contig112610 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:15386:25680_1:N:0:GGCTAC Contig65111 12336 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:2697:27461_1:N:0:GGCTAC Contig4832 2969 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:4285:27719_1:N:0:GGCTAC Contig117132 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:5911:27817_1:N:0:GGCTAC Contig23140 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:13013:28459_1:N:0:GGCTAC Contig84887 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:19702:30587_1:N:0:GGCTAC Contig148373 6480 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:5977:31466_1:N:0:GGCTAC Contig126469 3513 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:8218:35433_1:N:0:GGCTAC Contig100414 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:16055:36626_1:N:0:GGCTAC Contig93047 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:8325:43624_1:N:0:GGCTAC Contig35960 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:14875:44375_1:N:0:GGCTAC Contig173239 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:8631:45772_1:N:0:AGCTAC Contig128293 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:17139:47046_1:N:0:GGCTAC Contig199767 7404 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:9669:52618_1:N:0:GGCTAT Contig32939 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:19149:61639_1:N:0:GGCTAC Contig123907 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:1575:62781_1:N:0:GGCTAC Contig63594 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:5292:65122_1:N:0:GGCTAC Contig203883 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:1837:65724_1:N:0:GGCTAC Contig41141 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:11776:72310_1:N:0:GGCTAC Contig61683 2980 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:20053:73877_1:N:0:GGCTAC Contig137678 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:8866:75850_1:N:0:GGCTAC Contig119262 5588 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:3263:78249_1:N:0:GGCTAC Contig36147 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:6526:78009_1:N:0:GGCTAC Contig42324 21142 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:16175:83763_1:N:0:GGCTAC Contig61983 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:16894:86290_1:N:0:GGCTAC Contig104651 1095 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:5184:88127_1:N:0:GGCTAC Contig180633 1251 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:17837:95727_1:N:0:GGCTAC Contig2617 12614 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1105:13731:97021_1:N:0:GGCTAC Contig156590 11001 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:10921:2649_1:N:0:GGCTAC Contig48246 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:18224:3250_1:N:0:GGCTAC Contig37273 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:14330:3632_1:N:0:GGCTAC Contig47473 6623 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:18964:4779_1:N:0:GGCTAC Contig130046 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:8680:11493_1:N:0:GGCTAC Contig91741 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:5619:12648_1:N:0:GGCTAC Contig81827 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:13811:13704_1:N:0:GGCTAC Contig3092 10073 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:8369:14428_1:N:0:GGCTAC Contig209860 949 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:1130:19669_1:N:0:GGCTAC Contig90470 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:18599:21311_1:N:0:GGCTAC Contig173764 4968 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:8578:33017_1:N:0:GGCTAC Contig25359 19525 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:7330:33419_1:N:0:GGCTAC Contig137767 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:8540:34936_1:N:0:GGCTAC Contig196303 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:18524:35206_1:N:0:GGCTAC Contig207472 4279 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:14923:42113_1:N:0:GGCTAC Contig41227 4546 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:3582:42554_1:N:0:GGCTAC Contig49624 20987 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:5322:43011_1:N:0:GGCTAC Contig66921 11546 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:13409:43082_1:N:0:GGCTAC Contig8416 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:4722:47517_1:N:0:GGCTAC Contig123599 6157 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:19981:48597_1:N:0:GGCTAC Contig2617 12613 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:1931:53023_1:N:0:GGCTAC Contig90228 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:8727:53936_1:N:0:GGCTAC Contig145722 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:9537:53840_1:N:0:GGCTAC Contig55969 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:17791:55833_1:N:0:GGCTAC Contig92778 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:3284:56798_1:N:0:GGCTAC Contig6691 13041 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:4904:59525_1:N:0:GGCTAC Contig72295 29909 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:17227:59693_1:N:0:GGCTAC Contig115781 1505 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:12689:64107_1:N:0:GGCTAC Contig66462 6789 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:17437:64558_1:N:0:GGCTAC Contig90228 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:12915:64753_1:N:0:GGCTAC Contig136606 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:11426:68071_1:N:0:GGCTAC Contig62710 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:7433:68810_1:N:0:GGCTAC Contig26352 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:19813:69339_1:N:0:GGCTAC Contig96879 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:7152:72964_1:N:0:GGCTAC Contig39341 11943 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:12016:74342_1:N:0:GGCTAC Contig9137 6876 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:11813:74949_1:N:0:GGCTAC Contig173159 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:14493:79407_1:N:0:GGCTAC Contig139148 1485 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:13070:81936_1:N:0:GGCTAC Contig33284 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:11649:82799_1:N:0:GGCTAC Contig630886 7074 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:11054:83189_1:N:0:GGCTAC Contig47556 26304 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:5816:87480_1:N:0:GGCTAC Contig27574 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:4491:87616_1:N:0:GGCTAC Contig119316 1675 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:17900:90589_1:N:0:GGCTAC Contig29753 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:10707:94027_1:N:0:GGCTAC Contig8663 2292 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:12920:94811_1:N:0:GGCTAC Contig148105 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:7418:95221_1:N:0:GGCTAC Contig47095 6077 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1106:19235:97716_1:N:0:GGCTAC Contig99098 5091 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:9365:5222_1:N:0:GGCTAC Contig62712 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:7812:8852_1:N:0:GGCTAC Contig71648 2039 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:5840:10206_1:N:0:GGCTAC Contig133125 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:10271:10263_1:N:0:GGCTAC Contig66804 18354 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:18622:16775_1:N:0:GGCTAC Contig196877 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:14831:17144_1:N:0:GGCTAC Contig98561 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:2018:19274_1:N:0:GGCTAC Contig89993 3781 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:4937:19480_1:N:0:GGCTAC Contig142059 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:8589:20190_1:N:0:GGCTAC Contig99068 2734 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:1995:20401_1:N:0:GGCTAC Contig62092 7186 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:2547:22528_1:N:0:GGCTAC Contig148416 2204 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:5644:25669_1:N:0:GGCTAC Contig1281 24130 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:4137:25754_1:N:0:GGCTAC Contig189032 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:19566:28987_1:N:0:GGCTAC Contig5365 3509 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:11623:31948_1:N:0:GGCTAC Contig43261 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:7057:33473_1:N:0:GGCTAC Contig89854 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:1816:33762_1:N:0:GGCTAC Contig68105 5326 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:11387:33891_1:N:0:GGCTAC Contig158187 2533 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:19667:34880_1:N:0:GGCTAC Contig144013 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:20941:37871_1:N:0:GGCTAC Contig110429 2068 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:15916:38312_1:N:0:GGCTAC Contig98989 2027 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:19972:40264_1:N:0:GGCTAC Contig56583 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:21125:44607_1:N:0:GGCTAC Contig8416 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:9958:45553_1:N:0:GGCTAC Contig23033 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:3208:51624_1:N:0:GGCTAC Contig55427 2843 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:3427:51706_1:N:0:GGCTAC Contig108457 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:11751:52444_1:N:0:GGCTAC Contig110007 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:2908:53027_1:N:0:GGCTAC Contig82469 1411 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:13115:56749_1:N:0:GGCTAC Contig64125 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:7695:56855_1:N:0:GGCTAC Contig142286 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:13133:56753_1:N:0:GGCTAC Contig64125 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:15297:57680_1:N:0:GGCTAC Contig78973 4002 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:18146:58921_1:N:0:GGCTAC Contig88136 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:7536:61910_1:N:0:GGCTAC Contig97816 9622 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:6697:62242_1:N:0:GGCTAC Contig91350 1688 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:3167:66371_1:N:0:GGCTAC Contig61841 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:18713:67039_1:N:0:GGCTAC Contig138552 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:11648:67395_1:N:0:GGCTAC Contig59148 9662 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:2540:68711_1:N:0:GGCTAC Contig56887 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:18990:68835_1:N:0:GGCTAC Contig116697 2826 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:7460:71023_1:N:0:GGCTAC Contig86987 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:14029:72994_1:N:0:GGCTAC Contig129602 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:8431:73334_1:N:0:GGCTAC Contig81079 1464 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:13648:73422_1:N:0:GGCTAC Contig115301 3161 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:17381:77184_1:N:0:GGCTAC Contig228704 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:18759:78569_1:N:0:GGCTAC Contig121917 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:2119:79414_1:N:0:GGCTAC Contig170236 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:17760:82971_1:N:0:GGCTAC Contig406070 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:19043:83328_1:N:0:GGCTAC Contig207708 6789 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:16640:83805_1:N:0:GGCTAC Contig83826 2611 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:2540:86575_1:N:0:GGCTAC Contig127394 5034 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:14225:92270_1:N:0:GGCTAC Contig42420 2152 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:16060:92310_1:N:0:GGCTAC Contig75547 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:5651:93633_1:N:0:GGCTAC Contig136014 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1107:18525:96954_1:N:0:GGCTAC Contig88941 2994 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:11053:3243_1:N:0:GGCTAC Contig511367 1032 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:4305:5108_1:N:0:GGCTAC Contig107057 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:10746:6726_1:N:0:GGCTAC Contig27714 40106 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:10555:9399_1:N:0:GGCTAC Contig52161 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:12839:10468_1:N:0:GGCTAC Contig19048 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:7965:14663_1:N:0:GGCTAC Contig194503 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:1681:17451_1:N:0:GGCTAC Contig109787 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:21104:18197_1:N:0:GGCTAC Contig100464 14315 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:11896:22224_1:N:0:GGCTAC Contig4371 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:6509:25261_1:N:0:GGCTAC Contig122713 11724 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:17289:27335_1:N:0:GGCTAC Contig45274 10457 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:12545:28489_1:N:0:GGCTAC Contig95417 6865 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:12570:28515_1:N:0:GGCTAC Contig95417 6865 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:10737:28787_1:N:0:GGCTAC Contig116905 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:11068:30916_1:N:0:GGCTAC Contig146637 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:21146:33049_1:N:0:GGCTAC Contig166792 7295 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:2551:37360_1:N:0:GGCTAC Contig106883 2323 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:17956:38195_1:N:0:GGCTAC Contig127062 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:17630:38802_1:N:0:GGCTAC Contig133675 2901 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:1457:42554_1:N:0:GGCTAC Contig163104 2545 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:16930:42563_1:N:0:GGCTAC Contig32328 1066 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:10307:45186_1:N:0:GGCTAC Contig29352 4680 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:1228:45409_1:N:0:GGCTAC Contig90762 3373 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:14965:47401_1:N:0:GGCTAC Contig43591 13438 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:2148:48332_1:N:0:GGCTAC Contig8484 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:6725:51116_1:N:0:GGCTAC Contig1160 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:10149:53245_1:N:0:GGCTAC Contig37671 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:6909:53768_1:N:0:GGCTAC Contig61983 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:13508:55868_1:N:0:GGCTAC Contig34910 42156 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:17466:57705_1:N:0:GGCTAC Contig16497 17612 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:2458:58261_1:N:0:GGCTAA Contig63767 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:10358:64760_1:N:0:GGCTAC Contig15404 6577 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:2801:68919_1:N:0:GGCTAC Contig155981 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:1840:70801_1:N:0:GGCTAC Contig84096 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:9453:72891_1:N:0:GGCTAC Contig218481 19405 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:9960:73044_1:N:0:GGCTAC Contig17358 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:13551:74314_1:N:0:GGCTAC Contig128034 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:15603:77240_1:N:0:GGCTAC Contig199604 1413 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:13278:78607_1:N:0:GGCTAC Contig64001 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:14136:79608_1:N:0:GGCTAC Contig202466 4695 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:1715:82629_1:N:0:GGCTAC Contig64 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:10122:82691_1:N:0:GGCTAC Contig58022 1139 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:1405:82853_1:N:0:GGCTAC Contig145352 1543 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:6296:85521_1:N:0:GGCTAC Contig71397 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:2764:86626_1:N:0:GGCTAC Contig115512 1895 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:16994:92463_1:N:0:GGCTAC Contig75707 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:4993:93354_1:N:0:GGCTAC Contig47662 17678 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:1353:96348_1:N:0:GGCTAC Contig239362 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:4158:98462_1:N:0:GGCTAC Contig148681 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1108:18704:98970_1:N:0:GGCTAC Contig61457 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:3716:3008_1:N:0:GGCTAC Contig196877 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:1668:8694_1:N:0:GGCTAC Contig74619 4104 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:8384:9182_1:N:0:GGCTAC Contig108503 3177 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:4479:11384_1:N:0:GGCTAC Contig118962 1910 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:13448:12776_1:N:0:GGCTAC Contig97156 2613 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:13468:12781_1:N:0:GGCTAC Contig97156 2613 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:6136:16977_1:N:0:GGCTAC Contig167531 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:3552:19531_1:N:0:GGCTAC Contig8484 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:2735:23827_1:N:0:GGCTAC Contig165585 11280 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:20548:24585_1:N:0:GGCTAC Contig111658 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:1479:24850_1:N:0:GGCTAC Contig53243 7717 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:6956:25153_1:N:0:GGCTAC Contig10508 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:6160:26542_1:N:0:GGCTAC Contig92718 1234 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:18956:28346_1:N:0:GGCTAC Contig77095 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:6060:28839_1:N:0:GGCTAC Contig361 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:7494:32570_1:N:0:GGCAAC Contig318 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:10055:33300_1:N:0:GGCTAC Contig95684 2446 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:19394:33720_1:N:0:GGCTAC Contig50701 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:19945:35051_1:N:0:GGCTAC Contig113391 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:8508:39380_1:N:0:GGCTAC Contig15069 1467 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:18838:39302_1:N:0:GGCTAC Contig100381 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:20834:40766_1:N:0:GGCTAC Contig196877 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:5355:41972_1:N:0:GGCTAC Contig145063 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:18671:41879_1:N:0:GGCTAC Contig20989 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:15493:43076_1:N:0:GGCTAC Contig71457 3885 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:14472:43993_1:N:0:GGCTAC Contig147872 2 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:12535:46229_1:N:0:GGCTAC Contig99763 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:4693:50021_1:N:0:GGCTAC Contig51616 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:17287:57852_1:N:0:GGCTAC Contig1184 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:4557:59826_1:N:0:GGCTAC Contig70761 5161 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:16310:62749_1:N:0:GGCTAC Contig47232 19659 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:5297:63533_1:N:0:GGCTAC Contig686969 1558 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:16899:64892_1:N:0:GGCTAC Contig209263 1 Chromosomal sequence could not be extracted for HWI-D00743:54:C8MOMACXX:1:1109:1648:66407_1:N:0:GGCTAC Contig602905 1609 1000000 reads; of these: 1000000 (100.00%) were unpaired; of these: 371739 (37.17%) aligned 0 times 206430 (20.64%) aligned exactly 1 time 421831 (42.18%) aligned >1 times 62.83% overall alignment rate 1000000 reads; of these: 1000000 (100.00%) were unpaired; of these: 371388 (37.14%) aligned 0 times 205402 (20.54%) aligned exactly 1 time 423210 (42.32%) aligned >1 times 62.86% overall alignment rate Processed 1000000 sequences so far Successfully deleted the temporary file olur_bsseq_all_R1.fastq.gz_C_to_T.fastq Final Alignment report ====================== Sequences analysed in total: 1000000 Number of alignments with a unique best hit from the different alignments: 544525 Mapping efficiency: 54.5% Final Cytosine Methylation Report ================================= Total number of C's analysed: 4787053 Total methylated C's in CpG context: 242280 Total methylated C's in CHG context: 27803 Total methylated C's in CHH context: 54475 Total methylated C's in Unknown context: 1454 Total unmethylated C's in CpG context: 559772 Total unmethylated C's in CHG context: 977563 Total unmethylated C's in CHH context: 2925160 Total unmethylated C's in Unknown context: 17330 C methylated in CpG context: 30.2% C methylated in CHG context: 2.8% C methylated in CHH context: 1.8% C methylated in Unknown context (CN or CHN): 7.7% Bismark completed in 0d 0h 5m 41s ==================== Bismark run complete ====================