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/scrubbed/samwhite/data/P_generosa/Pgenerosa_v070/ (absolute path is '/gscratch/scrubbed/samwhite/data/P_generosa/Pgenerosa_v070/)' Processing sequences up to read no. 500000 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_geo_rrbs_bismark/subset_Pgenerosa_v070_500000'): /gscratch/scrubbed/samwhite/data/P_generosa/BSeq/rrbs/pgen_bsseq_all_R1.fastq.gz /gscratch/scrubbed/samwhite/data/P_generosa/BSeq/rrbs/pgen_bsseq_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_geo_rrbs_bismark/subset_Pgenerosa_v070_500000 Now reading in and storing sequence information of the genome specified in: /gscratch/scrubbed/samwhite/data/P_generosa/Pgenerosa_v070/ 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/P_generosa/BSeq/rrbs/pgen_bsseq_all_R1.fastq.gz and /gscratch/scrubbed/samwhite/data/P_generosa/BSeq/rrbs/pgen_bsseq_all_R2.fastq.gz Input files are in FastQ format Processing reads up to sequence no. 500000 from /gscratch/scrubbed/samwhite/data/P_generosa/BSeq/rrbs/pgen_bsseq_all_R1.fastq.gz Writing a C -> T converted version of the input file pgen_bsseq_all_R1.fastq.gz to pgen_bsseq_all_R1.fastq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file pgen_bsseq_all_R1.fastq.gz (500001 sequences in total) Processing reads up to sequence no. 500000 from /gscratch/scrubbed/samwhite/data/P_generosa/BSeq/rrbs/pgen_bsseq_all_R2.fastq.gz Writing a G -> A converted version of the input file pgen_bsseq_all_R2.fastq.gz to pgen_bsseq_all_R2.fastq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file pgen_bsseq_all_R2.fastq.gz (500001 sequences in total) Input files are pgen_bsseq_all_R1.fastq.gz_C_to_T.fastq and pgen_bsseq_all_R2.fastq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /gscratch/scrubbed/samwhite/data/P_generosa/Pgenerosa_v070/ 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 pgen_bsseq_all_R1.fastq.gz_C_to_T.fastq and pgen_bsseq_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: SL-HBW:624:CAAWVANXX:5:2301:1512:1956_1:N:0:ATCACG/1 99 PGA_scaffold25235__1_contigs__length_1316_CT_converted 580 1 50M = 580 -50 NGTTTATATGTATGTATTATATTTGTGTAGGTATTGTATTTGATAAGGAT #<<>> Writing bisulfite mapping results to pgen_bsseq_all_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/scrubbed/samwhite/data/P_generosa/BSeq/rrbs/pgen_bsseq_all_R1.fastq.gz and /gscratch/scrubbed/samwhite/data/P_generosa/BSeq/rrbs/pgen_bsseq_all_R2.fastq.gz Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:11623:2069_1:N:0:ATCACG PGA_scaffold32732__1_contigs__length_2240 3 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:15086:2208_1:N:0:ATCACG PGA_scaffold41319__1_contigs__length_1135 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:17208:2040_1:N:0:ATCACG PGA_scaffold71178__1_contigs__length_4197 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:13969:2647_1:N:0:ATCACG PGA_scaffold23407__1_contigs__length_2192 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:1609:3036_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:14032:3053_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:7726:3624_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:3973:3828_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4047:4144_1:N:0:ATCACG PGA_scaffold45488__1_contigs__length_1333 1237 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4971:4235_1:N:0:ATCACG PGA_scaffold52424__1_contigs__length_3527 3429 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:12517:4131_1:N:0:ATCACG PGA_scaffold20616__1_contigs__length_1183 1088 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:17368:4030_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:15997:4377_1:N:0:ATCACG PGA_scaffold67771__1_contigs__length_6483 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:14831:4639_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:3873:7275_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:6490:8347_1:N:0:ATCACG PGA_scaffold11450__1_contigs__length_1253 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:12727:9121_1:N:0:ATCACG PGA_scaffold65325__1_contigs__length_12743 12649 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:15388:9040_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:6448:9781_1:N:0:ATCACG PGA_scaffold19151__1_contigs__length_2082 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:12198:10107_1:N:0:ATCACG PGA_scaffold14256__1_contigs__length_1778 1704 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4811:11102_1:N:0:ATCACG PGA_scaffold30804__1_contigs__length_2641 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:12417:11389_1:N:0:ATCACG PGA_scaffold37296__1_contigs__length_1012 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:14680:11988_1:N:0:ATCACG PGA_scaffold34510__1_contigs__length_1314 1225 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4623:12077_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:13701:12308_1:N:0:ATCACG PGA_scaffold45254__1_contigs__length_1291 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:19459:12814_1:N:0:ATCACG PGA_scaffold25165__1_contigs__length_2707 2611 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:20626:13308_1:N:0:ATCACG PGA_scaffold61583__1_contigs__length_13650 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:9364:13583_1:N:0:ATCACG PGA_scaffold19863__1_contigs__length_1761 1669 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:20762:13651_1:N:0:ATCACG PGA_scaffold1564__1_contigs__length_1666 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:9736:14242_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:16275:14515_1:N:0:ATCACG PGA_scaffold20616__1_contigs__length_1183 1085 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:19467:15122_1:N:0:ATCACG PGA_scaffold36490__1_contigs__length_5243 3 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:20447:15349_1:N:0:ATCACG PGA_scaffold9226__1_contigs__length_1034 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:14907:16248_1:N:0:ATCACG PGA_scaffold56753__1_contigs__length_3010 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:15434:16045_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798926 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:7616:16737_1:N:0:GTCACG PGA_scaffold24917__1_contigs__length_1507 1415 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:13314:17737_1:N:0:ATCACG PGA_scaffold32803__1_contigs__length_2645 2555 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:5113:17810_1:N:0:ATCACG PGA_scaffold48397__1_contigs__length_20908 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:7001:20835_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:12053:21375_1:N:0:ATCACG PGA_scaffold34208__1_contigs__length_2237 2144 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4699:21694_1:N:0:ATCACG PGA_scaffold20616__1_contigs__length_1183 1087 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:20362:21666_1:N:0:ATCACG PGA_scaffold71472__1_contigs__length_4043 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:3979:21903_1:N:0:ATCACG PGA_scaffold50821__1_contigs__length_2343 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:6493:23041_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:6749:23611_1:N:0:ATCACG PGA_scaffold51538__1_contigs__length_9641 3 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:11861:23521_1:N:0:ATCACG PGA_scaffold71988__1_contigs__length_4570 4471 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:5886:24241_1:N:0:ATCACG PGA_scaffold30867__1_contigs__length_1516 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:11558:24481_1:N:0:ATCACG PGA_scaffold43189__1_contigs__length_2819 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:7504:24810_1:N:0:ATCACG PGA_scaffold22606__1_contigs__length_4570 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:19744:25783_1:N:0:ATCACG PGA_scaffold67542__1_contigs__length_23105 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:12371:26365_1:N:0:ATCACG PGA_scaffold955__1_contigs__length_1266 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:3323:26853_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:1977:27635_1:N:0:ATCACG PGA_scaffold34477__1_contigs__length_6039 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:1834:27730_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:10862:27989_1:N:0:ATCACG PGA_scaffold2516__1_contigs__length_2719 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:19571:31179_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798927 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:6874:31573_1:N:0:ATCACG PGA_scaffold14495__1_contigs__length_1124 1025 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:11200:31541_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:3159:31974_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:13870:31760_1:N:0:ATCACG PGA_scaffold71873__1_contigs__length_8186 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:5855:32292_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798927 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:7972:32861_1:N:0:AACACG PGA_scaffold25592__1_contigs__length_1155 1059 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4156:34487_1:N:0:ATCACG PGA_scaffold718__1_contigs__length_989392 989315 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:18692:34381_1:N:0:ATCACG PGA_scaffold59977__1_contigs__length_1141 1043 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:10665:34864_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:11790:36217_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:5437:36841_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:14829:36769_1:N:0:ATCACG PGA_scaffold48911__1_contigs__length_1808 1707 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:14324:37124_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:2101:37716_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:1316:38991_1:N:0:ATCACG PGA_scaffold259769__1_contigs__length_1744 1658 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:17418:40568_1:N:0:ATCACG PGA_scaffold56216__1_contigs__length_1445 1354 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:17480:40958_1:N:0:ATCACG PGA_scaffold38848__1_contigs__length_1094 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:8443:41491_1:N:0:ATCACG PGA_scaffold31185__1_contigs__length_1433 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:15029:41867_1:N:0:ATCACG PGA_scaffold2416__1_contigs__length_3481 3391 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:13775:42754_1:N:0:ATCACG PGA_scaffold35412__1_contigs__length_2376 2284 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4591:43018_1:N:0:ATCACG PGA_scaffold304912__1_contigs__length_1731 1630 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:15869:43273_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:1419:44486_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4210:44750_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4873:44657_1:N:0:ATCACG PGA_scaffold12622__1_contigs__length_2849 2750 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4479:45035_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4184:47037_1:N:0:ATCACG PGA_scaffold5839__1_contigs__length_1041 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:10957:47064_1:N:0:ATCACG PGA_scaffold71478__1_contigs__length_4197 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:14591:47734_1:N:0:ATCACG PGA_scaffold73092__1_contigs__length_8564 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:17699:47602_1:N:0:ATCACG PGA_scaffold61692__1_contigs__length_6562 6465 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:16038:48486_1:N:0:ATCACG PGA_scaffold17225__1_contigs__length_1255 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:18012:48374_1:N:0:ATCACG PGA_scaffold71790__1_contigs__length_1978 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:21106:48323_1:N:0:ATCACG PGA_scaffold47144__1_contigs__length_1542 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:9333:50092_1:N:0:ATCACG PGA_scaffold200540__1_contigs__length_1008 932 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:11392:50565_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:17882:51731_1:N:0:ATCACG PGA_scaffold11999__1_contigs__length_1106 1013 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:19654:51988_1:N:0:ATCACG PGA_scaffold72572__1_contigs__length_10914 10817 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:10934:52441_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:20120:52719_1:N:0:ATCACG PGA_scaffold48962__1_contigs__length_1318 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:13220:53499_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798925 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:9269:53509_1:N:0:ATCACG PGA_scaffold71823__1_contigs__length_4781 4694 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:17173:54382_1:N:0:ATCACG PGA_scaffold2268__1_contigs__length_1115 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:3717:54626_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:19470:54849_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:6417:55494_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798926 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:12261:55276_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:9171:56913_1:N:0:ATCACG PGA_scaffold44807__1_contigs__length_6413 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:14325:57744_1:N:0:ATCACG PGA_scaffold11716__1_contigs__length_4918 4827 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:5992:57751_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:13118:57835_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:14403:59437_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:3269:59533_1:N:0:ATCACG PGA_scaffold19606__1_contigs__length_3441 3345 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:8264:61818_1:N:0:ATCACG PGA_scaffold26918__1_contigs__length_2211 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:17936:62304_1:N:0:ATCACG PGA_scaffold51815__1_contigs__length_2058 3 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:5229:62868_1:N:0:ATCACG PGA_scaffold6577__1_contigs__length_5915 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:18114:63590_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:12256:64747_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:19152:65486_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:14112:66096_1:N:0:ATCACG PGA_scaffold47727__1_contigs__length_1041 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:6165:67152_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:9489:67390_1:N:0:ATCACG PGA_scaffold71843__1_contigs__length_9746 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:15544:67398_1:N:0:ATCACG PGA_scaffold48444__1_contigs__length_1488 1390 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:7597:67757_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:3357:68481_1:N:0:ATCACG PGA_scaffold52573__1_contigs__length_6599 6501 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:13324:70925_1:N:0:ATCACG PGA_scaffold15343__1_contigs__length_1664 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:10868:72754_1:N:0:ATCACG PGA_scaffold31553__1_contigs__length_1536 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:9726:76737_1:N:0:ATCACG PGA_scaffold32302__1_contigs__length_3672 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:10442:76898_1:N:0:ATCACG PGA_scaffold48962__1_contigs__length_1318 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:11389:76804_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:19568:76981_1:N:0:ATCACG PGA_scaffold26561__1_contigs__length_2654 2557 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4639:77748_1:N:0:ATCACG PGA_scaffold20815__1_contigs__length_1035 937 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:10580:78000_1:N:0:ATCACG PGA_scaffold43086__1_contigs__length_1587 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:19574:78139_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:9218:78409_1:N:0:ATCACG PGA_scaffold60718__1_contigs__length_9365 9268 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:1794:79104_1:N:0:ATCACG PGA_scaffold64242__1_contigs__length_4463 4364 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:13183:79132_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798927 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:9521:80297_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:13691:80511_1:N:0:ATCACG PGA_scaffold45306__1_contigs__length_4599 4504 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:3328:81619_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:7413:82454_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:2147:82634_1:N:0:ATCACG PGA_scaffold20616__1_contigs__length_1183 1088 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:19147:82724_1:N:0:ATCACG PGA_scaffold11795__1_contigs__length_2325 2232 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:6181:83001_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:15212:83388_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:15488:85331_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:16172:85307_1:N:0:ATCACG PGA_scaffold1826__1_contigs__length_1085 986 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:9300:85572_1:N:0:ATCACG PGA_scaffold30804__1_contigs__length_2641 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:9792:85978_1:N:0:ATCACG PGA_scaffold38376__1_contigs__length_3809 3754 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:18795:85865_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:4993:86839_1:N:0:ATCACG PGA_scaffold261067__1_contigs__length_1024 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:18071:87456_1:N:0:ATCACG PGA_scaffold51107__1_contigs__length_1707 1620 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:16622:87956_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:10919:88251_1:N:0:ATCACG PGA_scaffold54741__1_contigs__length_2470 2378 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:20298:88315_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798926 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:8279:91282_1:N:0:ATCACG PGA_scaffold35705__1_contigs__length_2009 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:8650:94304_1:N:0:ATCACG PGA_scaffold33858__1_contigs__length_1125 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:11318:94263_1:N:0:ATCACG PGA_scaffold59300__1_contigs__length_6746 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:5880:95163_1:N:0:ATCACG PGA_scaffold45889__1_contigs__length_3836 3746 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:11486:95295_1:N:0:ATCACG PGA_scaffold67742__1_contigs__length_1600 1508 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:9231:96450_1:N:0:ATCACG PGA_scaffold66423__1_contigs__length_8655 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:15151:96847_1:N:0:ATCACG PGA_scaffold240645__1_contigs__length_1308 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:11860:98087_1:N:0:ATCACG PGA_scaffold68968__1_contigs__length_28899 3 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:19038:98024_1:N:0:ATCACG PGA_scaffold1146__1_contigs__length_1066 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:7073:99028_1:N:0:ATCACG PGA_scaffold26966__1_contigs__length_6270 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:20403:100066_1:N:0:ATCACG PGA_scaffold3305__1_contigs__length_2675 2580 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2301:10373:100862_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:12533:2329_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:19534:2992_1:N:0:ATCACG PGA_scaffold34477__1_contigs__length_6039 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:16811:3185_1:N:0:ATCACG PGA_scaffold63395__1_contigs__length_9209 9119 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:6249:3692_1:N:0:ATCACG PGA_scaffold32403__1_contigs__length_2511 2411 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:15641:3757_1:N:0:ATCACG PGA_scaffold290947__1_contigs__length_6787 6688 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:9555:5478_1:N:0:ATCACG PGA_scaffold15845__1_contigs__length_13793 13701 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:16955:7587_1:N:0:ATCACG PGA_scaffold29359__1_contigs__length_8307 3 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:17169:7826_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:7453:8930_1:N:0:ATCACG PGA_scaffold2124__1_contigs__length_1167 1072 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:9223:8781_1:N:0:ATCACG PGA_scaffold25330__1_contigs__length_1946 1849 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:5103:12122_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:17444:12957_1:N:0:ATCACG PGA_scaffold55830__1_contigs__length_2500 2411 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:10698:14060_1:N:0:ATCACG PGA_scaffold70484__1_contigs__length_1579 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:20148:15215_1:N:0:ATCACG PGA_scaffold50593__1_contigs__length_7492 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:15402:15470_1:N:0:ATCACG PGA_scaffold70484__1_contigs__length_1579 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:12420:17869_1:N:0:ATCACG PGA_scaffold34477__1_contigs__length_6039 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:9160:18281_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:19748:18521_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:13330:19002_1:N:0:ATTACG PGA_scaffold19684__1_contigs__length_1235 1183 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:17613:20332_1:N:0:ATCACG PGA_scaffold20510__1_contigs__length_12130 12030 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:15046:21221_1:N:0:ATCACG PGA_scaffold69349__1_contigs__length_22993 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:14301:21559_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:8852:22850_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:20367:23292_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:20570:23348_1:N:0:ATCACG PGA_scaffold62114__1_contigs__length_4676 4579 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:16810:23592_1:N:0:ATCACG PGA_scaffold45254__1_contigs__length_1291 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:13093:24131_1:N:0:ATCACG PGA_scaffold34477__1_contigs__length_6039 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:20479:24779_1:N:0:ATCACG PGA_scaffold13912__1_contigs__length_3329 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:5534:25821_1:N:0:ATCACG PGA_scaffold41470__1_contigs__length_1243 1149 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:14563:26025_1:N:0:ATCACG PGA_scaffold37130__1_contigs__length_1146 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:8620:28439_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798927 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:16200:28469_1:N:0:GTCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:15886:28510_1:N:0:ATCACG PGA_scaffold16981__1_contigs__length_6088 5989 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:11189:29532_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:6736:32981_1:N:0:ATCACG PGA_scaffold16152__1_contigs__length_2981 2882 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:11250:33086_1:N:0:ATCACG PGA_scaffold22811__1_contigs__length_1003 902 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:5900:33644_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:1365:34113_1:N:0:ATCACG PGA_scaffold32599__1_contigs__length_1670 1575 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:16070:35494_1:N:0:ATCACG PGA_scaffold34477__1_contigs__length_6039 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:12877:36967_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:10960:38529_1:N:0:ATCACG PGA_scaffold2878__1_contigs__length_1507 1406 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:19835:39416_1:N:0:ATCACG PGA_scaffold26101__1_contigs__length_2017 1921 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:1727:40471_1:N:0:ATCACG PGA_scaffold55991__1_contigs__length_1093 997 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:20279:40693_1:N:0:ATCACG PGA_scaffold51244__1_contigs__length_2261 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:13368:41203_1:N:0:ATCACG PGA_scaffold14436__1_contigs__length_1387 1323 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:4144:42189_1:N:0:ATCACG PGA_scaffold38882__1_contigs__length_1565 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:14179:42955_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:3496:43657_1:N:0:ATCACG PGA_scaffold29430__1_contigs__length_1478 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:14761:44750_1:N:0:ATCACG PGA_scaffold32403__1_contigs__length_2511 2411 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:10684:45304_1:N:0:AACACG PGA_scaffold33344__1_contigs__length_1604 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:5371:45503_1:N:0:ATCACG PGA_scaffold45334__1_contigs__length_1842 1745 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:9952:45506_1:N:0:ATCACG PGA_scaffold45306__1_contigs__length_4599 4501 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:18882:46860_1:N:0:ATCACG PGA_scaffold7168__1_contigs__length_1398 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:7122:47640_1:N:0:ATCACG PGA_scaffold17490__1_contigs__length_1309 1211 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:9920:47990_1:N:0:ATCACG PGA_scaffold57422__1_contigs__length_21905 21807 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:9531:48233_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:2602:48508_1:N:0:ATCACG PGA_scaffold42004__1_contigs__length_1281 1186 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:10231:49684_1:N:0:ATCACG PGA_scaffold35239__1_contigs__length_5873 5773 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:17005:49851_1:N:0:ATCACG PGA_scaffold14495__1_contigs__length_1124 1026 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:14788:52898_1:N:0:ATCACG PGA_scaffold33019__1_contigs__length_2640 3 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:9191:53249_1:N:0:ATCACG PGA_scaffold15193__1_contigs__length_1344 3 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:5627:54173_1:N:0:ATCACG PGA_scaffold1738__1_contigs__length_1663 1565 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:10641:54471_1:N:0:ATCACG PGA_scaffold48962__1_contigs__length_1318 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:12635:55086_1:N:0:ATCACG PGA_scaffold600__1_contigs__length_3160 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:8286:55759_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:20097:55818_1:N:0:ATCACG PGA_scaffold32302__1_contigs__length_3672 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:9588:56395_1:N:0:ATCACG PGA_scaffold34691__1_contigs__length_1006 916 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:1514:58324_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:17683:58436_1:N:0:ATCACG PGA_scaffold66868__1_contigs__length_2274 2173 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:1430:59681_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:7308:60956_1:N:0:ATCACG PGA_scaffold50673__1_contigs__length_1711 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:14877:61279_1:N:0:ATCACG PGA_scaffold67336__1_contigs__length_15214 3 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:13414:61968_1:N:0:ATCACG PGA_scaffold64553__1_contigs__length_3217 3122 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:3281:62272_1:N:0:ATCACG PGA_scaffold35705__1_contigs__length_2009 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:4838:62870_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:17757:63199_1:N:0:ATCACG PGA_scaffold69659__1_contigs__length_2970 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:19371:63360_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:6302:65236_1:N:0:ATCACG PGA_scaffold34601__1_contigs__length_1043 956 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:11964:65208_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:15520:65730_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:3665:66461_1:N:0:ATCACG PGA_scaffold31199__1_contigs__length_2911 2819 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:19952:68417_1:N:0:ATCACG PGA_scaffold26101__1_contigs__length_2017 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:18899:69268_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:8116:69592_1:N:0:ATCACG PGA_scaffold48962__1_contigs__length_1318 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:11253:70246_1:N:0:ATCACG PGA_scaffold35093__1_contigs__length_1923 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:6789:71349_1:N:0:ATCACG PGA_scaffold157384__1_contigs__length_5567 5474 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:14396:71434_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:13743:72629_1:N:0:ATCACG PGA_scaffold23848__1_contigs__length_2302 2206 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:6071:73121_1:N:0:ATCACG PGA_scaffold25202__1_contigs__length_1156 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:6942:73017_1:N:0:ATCACG PGA_scaffold16016__1_contigs__length_12541 12443 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:12802:73186_1:N:0:ATCACG PGA_scaffold56753__1_contigs__length_3010 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:7098:74463_1:N:0:ATCACG PGA_scaffold184062__1_contigs__length_5550 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:1907:74783_1:N:0:ATCACG PGA_scaffold303430__1_contigs__length_2178 2084 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:14580:75541_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:15614:76257_1:N:0:ATCACG PGA_scaffold5248__1_contigs__length_2420 2324 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:16674:78112_1:N:0:ATCACG PGA_scaffold48962__1_contigs__length_1318 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:10663:78403_1:N:0:ATCACG PGA_scaffold34477__1_contigs__length_6039 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:6977:80902_1:N:0:ATCACG PGA_scaffold42006__1_contigs__length_1695 1599 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:18816:80981_1:N:0:ATCACG PGA_scaffold17225__1_contigs__length_1255 3 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:9978:81185_1:N:0:ATCACG PGA_scaffold70909__1_contigs__length_2936 2851 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:4984:81421_1:N:0:ATCACG PGA_scaffold13222__1_contigs__length_1862 1764 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:16541:81879_1:N:0:ATCACG PGA_scaffold48962__1_contigs__length_1318 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:9818:82529_1:N:0:ATCACG PGA_scaffold59169__1_contigs__length_14356 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:19182:84543_1:N:0:ATCACG PGA_scaffold59192__1_contigs__length_14185 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:1114:86246_1:N:0:ATCACG PGA_scaffold19498__1_contigs__length_3093 2995 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:5972:86568_1:N:0:ATCACG PGA_scaffold69599__1_contigs__length_2823 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:11512:86664_1:N:0:ATCACG PGA_scaffold58745__1_contigs__length_9856 9765 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:9827:89829_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:11217:91219_1:N:0:ATCACG PGA_scaffold34477__1_contigs__length_6039 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:18366:93170_1:N:0:ATCACG PGA_scaffold37332__1_contigs__length_1113 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:18364:93308_1:N:0:ATCACG PGA_scaffold35187__1_contigs__length_3059 2959 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:19407:93355_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:8414:93687_1:N:0:ATCACG PGA_scaffold43611__1_contigs__length_18859 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:19912:93903_1:N:0:ATCACG PGA_scaffold14069__1_contigs__length_1731 1632 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:10045:94746_1:N:0:ATCACG PGA_scaffold3992__1_contigs__length_4243 4146 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:8315:95341_1:N:0:ATCACG PGA_scaffold49882__1_contigs__length_1026 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:15583:95741_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798939 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:15754:96295_1:N:0:ATCACG PGA_scaffold3302__1_contigs__length_1089 994 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:2151:96846_1:N:0:ATCACG PGA_scaffold44297__1_contigs__length_8044 7945 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:5215:96874_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:1828:97656_1:N:0:ATCACG PGA_scaffold20616__1_contigs__length_1183 1088 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:8655:98540_1:N:0:ATCACG PGA_scaffold53886__1_contigs__length_1734 1637 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2304:9368:99394_1:N:0:ATCACG PGA_scaffold69502__1_contigs__length_1900 1806 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:8067:2505_1:N:0:ATCACG PGA_scaffold65517__1_contigs__length_15888 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:11615:2843_1:N:0:ATCACG PGA_scaffold69629__1_contigs__length_4117 4028 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:12359:7001_1:N:0:ATCACG PGA_scaffold66423__1_contigs__length_8655 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:9783:7289_1:N:0:ATCACG PGA_scaffold66423__1_contigs__length_8655 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:17443:7986_1:N:0:ATCACG PGA_scaffold48962__1_contigs__length_1318 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:19947:8931_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:20229:10178_1:N:0:ATCACG PGA_scaffold20616__1_contigs__length_1183 1087 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:1834:10768_1:N:0:ATCACG PGA_scaffold58103__1_contigs__length_5536 5435 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:5839:11188_1:N:0:ATCACG PGA_scaffold34477__1_contigs__length_6039 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:5861:11347_1:N:0:ATCACG PGA_scaffold21253__1_contigs__length_1081 983 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:16334:13051_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:15833:13974_1:N:0:ATCACG PGA_scaffold312267__1_contigs__length_6211 6123 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:12852:16739_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798928 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:7893:18201_1:N:0:ATCACG PGA_scaffold9703__1_contigs__length_4238 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:3113:19774_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:18294:20398_1:N:0:ATCACG PGA_scaffold63257__1_contigs__length_1801 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:7519:21858_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:12617:22414_1:N:0:ATCACG PGA_scaffold994__1_contigs__length_1026 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:10367:23498_1:N:0:ATCACG PGA_scaffold65226__1_contigs__length_2438 2339 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:13246:24784_1:N:0:ATCACG PGA_scaffold48498__1_contigs__length_32874 32782 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:7361:25103_1:N:0:ATCACG PGA_scaffold63040__1_contigs__length_10823 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:12437:25294_1:N:0:ATCACG PGA_scaffold48962__1_contigs__length_1318 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:19229:28321_1:N:0:ATCACG PGA_scaffold63603__1_contigs__length_6671 6573 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:8326:29245_1:N:0:ATGACG PGA_scaffold47219__1_contigs__length_2018 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:4462:29297_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:2916:31521_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:2664:32133_1:N:0:ATCACG PGA_scaffold56269__1_contigs__length_1703 1609 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:10646:32775_1:N:0:ATCACG PGA_scaffold31977__1_contigs__length_4172 3 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:2303:35370_1:N:0:ATCACG PGA_scaffold68466__1_contigs__length_1698 1 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:9444:36270_1:N:0:ATCACG PGA_scaffold323__1_contigs__length_1799026 1798929 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:14697:36994_1:N:0:ATCACG PGA_scaffold22663__1_contigs__length_3248 3 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:12285:37392_1:N:0:ATCACG PGA_scaffold35705__1_contigs__length_2009 2 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:2734:39446_1:N:0:ATCACG PGA_scaffold40087__1_contigs__length_4774 4686 Chromosomal sequence could not be extracted for SL-HBW:624:CAAWVANXX:5:2306:12952:39630_1:N:0:ATCACG PGA_scaffold51538__1_contigs__length_9641 1 500000 reads; of these: 500000 (100.00%) were paired; of these: 237478 (47.50%) aligned concordantly 0 times 99265 (19.85%) aligned concordantly exactly 1 time 163257 (32.65%) aligned concordantly >1 times 52.50% overall alignment rate 500000 reads; of these: 500000 (100.00%) were paired; of these: 235340 (47.07%) aligned concordantly 0 times 100217 (20.04%) aligned concordantly exactly 1 time 164443 (32.89%) aligned concordantly >1 times 52.93% overall alignment rate Processed 500000 sequences in total Successfully deleted the temporary files pgen_bsseq_all_R1.fastq.gz_C_to_T.fastq and pgen_bsseq_all_R2.fastq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 500000 Final Cytosine Methylation Report ================================= Total number of C's analysed: 8981086 Total methylated C's in CpG context: 274686 Total methylated C's in CHG context: 39211 Total methylated C's in CHH context: 71259 Total methylated C's in Unknown context: 1270 Total unmethylated C's in CpG context: 1036067 Total unmethylated C's in CHG context: 1879786 Total unmethylated C's in CHH context: 5680077 Total unmethylated C's in Unknown context: 17131 C methylated in CpG context: 21.0% C methylated in CHG context: 2.0% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 6.9% Bismark completed in 0d 0h 7m 17s ==================== Bismark run complete ====================