Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.5.2])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools found here: '/modules/uri_apps/software/SAMtools/1.14-GCC-11.2.0/bin/samtools'
Reference genome folder provided is ../data/ (absolute path is '/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/data/)'
FastQ format assumed (by default)
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
Each Bowtie 2 instance is going to be run with 48 threads. Please monitor performance closely and tune down if necessary!
Input files to be analysed (in current folder '/scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/code'):
../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-178-TP2_S1_R1_001.fastq.gz
../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-178-TP2_S1_R2_001.fastq.gz
Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported
Output will be written into the directory: /scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/output/08-Apul-WGBS/bismark_cutadapt/
Setting parallelization to single-threaded (default)
Summary of all aligner options: -q --score-min L,0,-1.0 -p 48 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Current working directory is: /scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/code
Now reading in and storing sequence information of the genome specified in: /scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/data/
Single-core mode: setting pid to 1
Paired-end alignments will be performed
=======================================
The provided filenames for paired-end alignments are ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-178-TP2_S1_R1_001.fastq.gz and ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-178-TP2_S1_R2_001.fastq.gz
Input files are in FastQ format
Writing a C -> T converted version of the input file trimmed_ACR-178-TP2_S1_R1_001.fastq.gz to trimmed_ACR-178-TP2_S1_R1_001.fastq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file trimmed_ACR-178-TP2_S1_R1_001.fastq.gz to trimmed_ACR-178-TP2_S1_R1_001.fastq.gz_G_to_A.fastq
Created C -> T as well as G -> A converted versions of the FastQ file trimmed_ACR-178-TP2_S1_R1_001.fastq.gz (182967324 sequences in total)
Writing a C -> T converted version of the input file trimmed_ACR-178-TP2_S1_R2_001.fastq.gz to trimmed_ACR-178-TP2_S1_R2_001.fastq.gz_C_to_T.fastq
Writing a G -> A converted version of the input file trimmed_ACR-178-TP2_S1_R2_001.fastq.gz to trimmed_ACR-178-TP2_S1_R2_001.fastq.gz_G_to_A.fastq
Created C -> T as well as G -> A converted versions of the FastQ file trimmed_ACR-178-TP2_S1_R2_001.fastq.gz (182967324 sequences in total)
Input files are trimmed_ACR-178-TP2_S1_R1_001.fastq.gz_C_to_T.fastq and trimmed_ACR-178-TP2_S1_R1_001.fastq.gz_G_to_A.fastq and trimmed_ACR-178-TP2_S1_R2_001.fastq.gz_C_to_T.fastq and trimmed_ACR-178-TP2_S1_R2_001.fastq.gz_G_to_A.fastq (FastQ)
Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /scratch3/workspace/zdellaert_uri_edu-deep_dive/deep-dive-expression/D-Apul/data/ with the specified options: -q --score-min L,0,-1.0 -p 48 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from trimmed_ACR-178-TP2_S1_R1_001.fastq.gz_C_to_T.fastq and trimmed_ACR-178-TP2_S1_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.0 -p 48 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
Found first alignment:
LH00260:131:22L7V3LT4:3:1101:3581:1014_1:N:0:GTCGGAGC+TNATAACC/1 77 * 0 0 * * 0 0 ANATAATTTTTTTTGTAAAATATTATATATTAAAATTTTAATTTAATTTTTAATAAAATATTATAAAAAATATAATATTTATTAAAAAATTATTAAAATTTATTAATTTTTTTAAAATAAATAATTTTTTTGAGT I#IIIII9IIII9IIII9IIIIII9I9IIIIIIIIIIIIIIIII9IIIIIII-IIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII-IIIIIIIII9IIIII9IIIIIII-I9IIIII9II YT:Z:UP
LH00260:131:22L7V3LT4:3:1101:3581:1014_2:N:0:GTCGGAGC+TNATAACC/2 141 * 0 0 * * 0 0 ACTCAAAAAAATTATTTATTTTAAAAAAATTAATAAATTTTAATAATTTTTTCATAAATATTATATTTTTTATAATATTTTATTAAAAATTAAATTAAAATTTTAATATATAATATTTTAAAAAAAAAATTATTT IIIIIII99IIIIIIIIIIIIIIIIIIIIIII-II-III9IIIIII99II999II9-9III9999I9I-III-9-9999-99I-9-I-999III99--9-999I999II9I999I9-I99-9III-9II99III9 YT:Z:UP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from trimmed_ACR-178-TP2_S1_R1_001.fastq.gz_G_to_A.fastq and trimmed_ACR-178-TP2_S1_R2_001.fastq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1.0 -p 48 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc))
Found first alignment:
LH00260:131:22L7V3LT4:3:1101:3581:1014_1:N:0:GTCGGAGC+TNATAACC/1 99 ptg000059l_GA_converted 1563633 1 130M1D5M = 1563869 372 ANACAACTTTTTCTACAAAATACCATACACTAAAATTTTAACCCAATTTTTAACAAAATATTACAAAAAATATAACATTTACTAAAAAACCACCAAAACTTATCAATCTCCTCAAAATAAACAACTTTTTTAAAT I#IIIII9IIII9IIII9IIIIII9I9IIIIIIIIIIIIIIIII9IIIIIII-IIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII-IIIIIIIII9IIIII9IIIIIII-I9IIIII9II AS:i:-21 XS:i:-21 XN:i:0 XM:i:3 XO:i:1 XG:i:1 NM:i:4 MD:Z:1A128^C2C1A0 YS:i:-32 YT:Z:CP
LH00260:131:22L7V3LT4:3:1101:3581:1014_2:N:0:GTCGGAGC+TNATAACC/2 147 ptg000059l_GA_converted 1563869 1 130M1D5M = 1563633 -372 AAACAACTTTTTCTTCAAAATACCATACACTAAAATTTTAACCCAATTTTTAACAAAATATTACAAAAAATATAACATTTACAAAAAAACCACCAAAACTTATCAATCTCCTCAAAATAAACAACTTTTTTAAAT 9III99II9-III9-99I-9I999I9II999I999-9--99III999-I-9-I99-9999-9-III-I9I9999III9-9II999II99IIIIII9III-II-IIIIIIIIIIIIIIIIIIIIIII99IIIIIII AS:i:-32 XS:i:-38 XN:i:0 XM:i:4 XO:i:1 XG:i:1 NM:i:5 MD:Z:14A67T47^C2C1A0 YS:i:-21 YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from trimmed_ACR-178-TP2_S1_R1_001.fastq.gz_G_to_A.fastq and trimmed_ACR-178-TP2_S1_R2_001.fastq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-1.0 -p 48 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
Found first alignment:
LH00260:131:22L7V3LT4:3:1101:3581:1014_1:N:0:GTCGGAGC+TNATAACC/1 83 ptg000006l_CT_converted 3066 1 5M1D130M = 2830 -372 ATTTAAAAAAGTTGTTTATTTTGAGGAGATTGATAAGTTTTGGTGGTTTTTTAGTAAATGTTATATTTTTTGTAATATTTTGTTAAAAATTGGGTTAAAATTTTAGTGTATGGTATTTTGTAGAAAAAGTTGTNT II9IIIII9I-IIIIIII9IIIII9IIIIIIIII-IIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIII9II9IIIIIIIII-IIIIIII9IIIIIIIIIIIIIIIII9I9IIIIII9IIII9IIII9IIIII#I AS:i:-21 XS:i:-19 XN:i:0 XM:i:3 XO:i:1 XG:i:1 NM:i:4 MD:Z:0T1G2^G128T1 YS:i:-32 YT:Z:CP
LH00260:131:22L7V3LT4:3:1101:3581:1014_2:N:0:GTCGGAGC+TNATAACC/2 163 ptg000006l_CT_converted 2830 1 5M1D130M = 3066 372 ATTTAAAAAAGTTGTTTATTTTGAGGAGATTGATAAGTTTTGGTGGTTTTTTTGTAAATGTTATATTTTTTGTAATATTTTGTTAAAAATTGGGTTAAAATTTTAGTGTATGGTATTTTGAAGAAAAAGTTGTTT IIIIIII99IIIIIIIIIIIIIIIIIIIIIII-II-III9IIIIII99II999II9-9III9999I9I-III-9-9999-99I-9-I-999III99--9-999I999II9I999I9-I99-9III-9II99III9 AS:i:-32 XS:i:-32 XN:i:0 XM:i:4 XO:i:1 XG:i:1 NM:i:5 MD:Z:0T1G2^G47A67T14 YS:i:-21 YT:Z:CP
Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from trimmed_ACR-178-TP2_S1_R1_001.fastq.gz_C_to_T.fastq and trimmed_ACR-178-TP2_S1_R2_001.fastq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.0 -p 48 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw))
Found first alignment:
LH00260:131:22L7V3LT4:3:1101:3581:1014_1:N:0:GTCGGAGC+TNATAACC/1 77 * 0 0 * * 0 0 ANATAATTTTTTTTGTAAAATATTATATATTAAAATTTTAATTTAATTTTTAATAAAATATTATAAAAAATATAATATTTATTAAAAAATTATTAAAATTTATTAATTTTTTTAAAATAAATAATTTTTTTGAGT I#IIIII9IIII9IIII9IIIIII9I9IIIIIIIIIIIIIIIII9IIIIIII-IIIIIIIII9II9IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII-IIIIIIIII9IIIII9IIIIIII-I9IIIII9II YT:Z:UP
LH00260:131:22L7V3LT4:3:1101:3581:1014_2:N:0:GTCGGAGC+TNATAACC/2 141 * 0 0 * * 0 0 ACTCAAAAAAATTATTTATTTTAAAAAAATTAATAAATTTTAATAATTTTTTCATAAATATTATATTTTTTATAATATTTTATTAAAAATTAAATTAAAATTTTAATATATAATATTTTAAAAAAAAAATTATTT IIIIIII99IIIIIIIIIIIIIIIIIIIIIII-II-III9IIIIII99II999II9-9III9999I9I-III-9-9999-99I-9-I-999III99--9-999I999II9I999I9-I99-9III-9II99III9 YT:Z:UP
>>> Writing bisulfite mapping results to trimmed_ACR-178-TP2_S1_pe.bam <<<
Reading in the sequence files ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-178-TP2_S1_R1_001.fastq.gz and ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-178-TP2_S1_R2_001.fastq.gz
Processed 1000000 sequence pairs so far
Processed 2000000 sequence pairs so far
Processed 3000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1117:30771:22278_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625590
Processed 4000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1119:13786:13523_1:N:0:GTCGGAGC+TTATAACC ptg000061l 2
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1120:29218:7486_1:N:0:GTCGGAGC+TTATAACC ptg000123l 44453
Processed 5000000 sequence pairs so far
Processed 6000000 sequence pairs so far
Processed 7000000 sequence pairs so far
Processed 8000000 sequence pairs so far
Processed 9000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1143:43322:16381_1:N:0:GTCGGAGC+TTATAACC ptg000146l 1
Processed 10000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1148:23294:12192_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572
Processed 11000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1149:15493:16451_1:N:0:GTCGGAGC+TTATAACC ptg000061l 250124
Processed 12000000 sequence pairs so far
Processed 13000000 sequence pairs so far
Processed 14000000 sequence pairs so far
Processed 15000000 sequence pairs so far
Processed 16000000 sequence pairs so far
Processed 17000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1177:11042:10371_1:N:0:GTCGGAGC+TTATAACC ptg000007l 12295874
Processed 18000000 sequence pairs so far
Processed 19000000 sequence pairs so far
Processed 20000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1185:17905:24043_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572
Processed 21000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1193:33361:19308_1:N:0:GTCGGAGC+TTATAACC ptg000093l 1
Processed 22000000 sequence pairs so far
Processed 23000000 sequence pairs so far
Processed 24000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1205:19240:6715_1:N:0:GTCGGAGC+TTATAACC ptg000039l 1
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1207:43832:11800_1:N:0:GTCGGAGC+TTATAACC ptg000093l 1
Processed 25000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1211:39681:19406_1:N:0:GTCGGAGC+TTATAACC ptg000109l 39608
Processed 26000000 sequence pairs so far
Processed 27000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1217:26919:14209_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625591
Processed 28000000 sequence pairs so far
Processed 29000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1229:37035:23539_1:N:0:GTCGGAGC+TTATAACC ptg000122l 47625
Processed 30000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1230:44739:14574_1:N:0:GTCGGAGC+TTATAACC ptg000152l 21001
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1231:26766:7948_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572
Processed 31000000 sequence pairs so far
Processed 32000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1242:16068:14672_1:N:0:GTCGGAGC+TTATAACC ptg000056l 2
Processed 33000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1245:6705:12977_1:N:0:GTCGGAGC+TTATAACC ptg000093l 1
Processed 34000000 sequence pairs so far
Processed 35000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1252:38580:1140_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625667
Processed 36000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1257:7587:18706_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1257:7579:18720_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572
Processed 37000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1263:12491:9601_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625579
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1263:16545:23146_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625654
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1264:33822:12010_1:N:0:GTCGGAGC+TTATAACC ptg000093l 1
Processed 38000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1264:40110:23034_1:N:0:GTCGGAGC+TTATAACC ptg000109l 39583
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1265:29760:12066_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625624
Processed 39000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1268:15080:22460_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625625
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1269:3784:7696_1:N:0:GTCGGAGC+TTATAACC ptg000093l 1
Processed 40000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1276:16796:4894_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625613
Processed 41000000 sequence pairs so far
Processed 42000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1282:17743:12725_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625629
Processed 43000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1288:8404:4516_1:N:0:GTCGGAGC+TTATAACC ptg000008l 38432908
Processed 44000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1292:21651:15344_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1292:21643:15358_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572
Processed 45000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1295:6001:28063_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625632
Processed 46000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1296:17476:25990_1:N:0:GTCGGAGC+TTATAACC ptg000118l 34333
Processed 47000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1303:22363:24981_1:N:0:GTCAGAGC+TTATAACC ptg000122l 1
Processed 48000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1308:4561:2429_1:N:0:GTCGGAGC+TTATAACC ptg000117l 29997
Processed 49000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1311:28692:26522_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625584
Processed 50000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1317:48720:19364_1:N:0:GTCGGAGC+TTATAACC ptg000109l 39662
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1319:18018:28105_1:N:0:GTCGGAGC+TTATAACC ptg000146l 1
Processed 51000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1321:50856:29562_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625621
Processed 52000000 sequence pairs so far
Processed 53000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1331:7911:22796_1:N:0:GTCGGAGC+TTATAACC ptg000015l 14997081
Processed 54000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1338:23869:2429_1:N:0:GTCGGAGC+TTATAACC ptg000109l 39583
Processed 55000000 sequence pairs so far
Processed 56000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1344:33053:1378_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625631
Processed 57000000 sequence pairs so far
Processed 58000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1354:25252:13341_1:N:0:GTCGGAGC+TTATAACC ptg000090l 1
Processed 59000000 sequence pairs so far
Processed 60000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1359:41008:16885_1:N:0:GTCGGAGC+TTATAACC ptg000109l 39590
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1361:18528:28231_1:N:0:GTCGGAGC+TTATAACC ptg000045l 1
Processed 61000000 sequence pairs so far
Processed 62000000 sequence pairs so far
Processed 63000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1374:12968:12080_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572
Processed 64000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1378:50905:17375_1:N:0:GTCGGAGC+TTATAACC ptg000090l 1
Processed 65000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1380:28578:20135_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625627
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1383:14223:4390_1:N:0:GTCGGAGC+TTATAACC ptg000174l 27214
Processed 66000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1384:33142:11926_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625658
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1384:14037:14069_1:N:0:GTCGGAGC+TTATAACC ptg000122l 1
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1385:50654:21675_1:N:0:GTCGGAGC+TTATAACC ptg000127l 27792
Processed 67000000 sequence pairs so far
Processed 68000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1393:32503:27545_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625625
Processed 69000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1396:13260:8382_1:N:0:GTCGGAGC+TTATAACC ptg000122l 1
Processed 70000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1403:34842:23216_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625593
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1407:33596:2737_1:N:0:GTCGGAGC+TTATAACC ptg000007l 12295881
Processed 71000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1407:28190:7920_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625629
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1407:9246:22362_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625584
Processed 72000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1411:30067:18426_1:N:0:GTCGGAGC+TTATAACC ptg000027l 1
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1413:37277:24687_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625590
Processed 73000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1418:50800:6043_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1418:14724:8060_1:N:0:GTCGGAGC+TTATAACC ptg000061l 1
Processed 74000000 sequence pairs so far
Processed 75000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1426:42837:8032_1:N:0:GTCGGAGC+TTATAACC ptg000093l 1
Processed 76000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1429:39033:22096_1:N:0:GTCGGAGC+TTATAACC ptg000061l 2
Processed 77000000 sequence pairs so far
Processed 78000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1440:6721:7794_1:N:0:GTCGGAGC+TTATAACC ptg000174l 27214
Processed 79000000 sequence pairs so far
Processed 80000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1448:49537:11534_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625625
Processed 81000000 sequence pairs so far
Processed 82000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1454:26466:19000_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625615
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1455:27939:26088_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625628
Processed 83000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1458:39988:1840_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625658
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1459:25965:29086_1:N:0:GTCGGAGC+TTATAACC ptg000015l 14997064
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1461:19636:14742_1:N:0:GTCGGAGC+TTATAACC ptg000125l 18853
Processed 84000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1465:49861:7219_1:N:0:GTCGGAGC+TTATAACC ptg000093l 1
Processed 85000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1468:49618:12206_1:N:0:GTCGGAGC+TTATAACC ptg000146l 3
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1469:35967:4096_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625628
Processed 86000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1473:31095:27012_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572
Processed 87000000 sequence pairs so far
Processed 88000000 sequence pairs so far
Processed 89000000 sequence pairs so far
Processed 90000000 sequence pairs so far
Processed 91000000 sequence pairs so far
Processed 92000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1495:21239:15162_1:N:0:GTCGGAGC+TTATAACC ptg000127l 27810
Processed 93000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:1497:28732:27461_1:N:0:GTCGGAGC+TTATAACC ptg000006l 2
Processed 94000000 sequence pairs so far
Processed 95000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2111:17201:10469_1:N:0:GTCGGAGC+TTATAACC ptg000093l 1
Processed 96000000 sequence pairs so far
Processed 97000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2123:42537:26088_1:N:0:GTCGGAGC+TTATAACC ptg000061l 250129
Processed 98000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2128:2756:5440_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625612
Processed 99000000 sequence pairs so far
Processed 100000000 sequence pairs so far
Processed 101000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2141:39470:15372_1:N:0:GTCGGAGC+TTATAACC ptg000122l 1
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2141:39487:15372_1:N:0:GTCGGAGC+TTATAACC ptg000122l 1
Processed 102000000 sequence pairs so far
Processed 103000000 sequence pairs so far
Processed 104000000 sequence pairs so far
Processed 105000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2158:44868:2975_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625581
Processed 106000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2162:48194:9909_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572
Processed 107000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2163:7692:28553_1:N:0:GTCGGAGC+TTATAACC ptg000090l 1
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2165:28934:26074_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625616
Processed 108000000 sequence pairs so far
Processed 109000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2174:13203:27783_1:N:0:GTCGGAGC+TTATAACC ptg000069l 259811
Processed 110000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2175:24856:5006_1:N:0:GTCGGAGC+TTATAACC ptg000056l 1
Processed 111000000 sequence pairs so far
Processed 112000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2186:27211:5833_1:N:0:GTCGGAGC+TTATAACC ptg000146l 2
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2186:27219:5847_1:N:0:GTCGGAGC+TTATAACC ptg000146l 2
Processed 113000000 sequence pairs so far
Processed 114000000 sequence pairs so far
Processed 115000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2195:7878:17081_1:N:0:GTCGGAGC+TTATAACC ptg000130l 1
Processed 116000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2203:15615:28119_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625666
Processed 117000000 sequence pairs so far
Processed 118000000 sequence pairs so far
Processed 119000000 sequence pairs so far
Processed 120000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2220:34874:12711_1:N:0:ATCGGAGC+TTATAACC ptg000082l 2
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2222:4633:27853_1:N:0:GTCGGAGC+TTATAACC ptg000153l 25739
Processed 121000000 sequence pairs so far
Processed 122000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2228:11382:18356_1:N:0:GTCGGAGC+TTATAACC ptg000146l 1
Processed 123000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2234:20462:4432_1:N:0:GTCGGAGC+TTATAACC ptg000093l 1
Processed 124000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2237:36315:19322_1:N:0:GTCGGAGC+TTATAACC ptg000117l 30013
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2238:46211:17235_1:N:0:GTCGGAGC+TTATAACC ptg000025l 21443060
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2239:28052:25920_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625600
Processed 125000000 sequence pairs so far
Processed 126000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2248:34308:1364_1:N:0:GTCGGAGC+TTATCACC ptg000033l 2625629
Processed 127000000 sequence pairs so far
Processed 128000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2257:13235:10441_1:N:0:GTCGGAGC+TTATAACC ptg000109l 39605
Processed 129000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2262:38208:19238_1:N:0:GTCGGAGC+TTATAACC ptg000007l 12295841
Processed 130000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2266:11318:27349_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625637
Processed 131000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2270:26766:16325_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625590
Processed 132000000 sequence pairs so far
Processed 133000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2277:13066:16815_1:N:0:GTCGGAGC+TTATAACC ptg000146l 2
Processed 134000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2281:41040:25878_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625615
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2281:41057:25878_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625615
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2281:41032:25892_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625615
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2281:41048:25892_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625615
Processed 135000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2285:46567:9251_1:N:0:GTCGGAGC+TTATAACC ptg000030l 2
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2285:13235:14588_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625627
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2287:3339:13285_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625658
Processed 136000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2289:29161:8424_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625570
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2289:51139:8760_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625570
Processed 137000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2297:42198:7261_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625577
Processed 138000000 sequence pairs so far
Processed 139000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2309:45604:16605_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625577
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2309:6001:29436_1:N:0:ATCGGAGC+TTATAACC ptg000033l 2625688
Processed 140000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2311:17913:6715_1:N:0:GTCGGAGC+TTATAACC ptg000093l 1
Processed 141000000 sequence pairs so far
Processed 142000000 sequence pairs so far
Processed 143000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2325:51431:3465_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625628
Processed 144000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2330:38977:14938_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625573
Processed 145000000 sequence pairs so far
Processed 146000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2339:27923:4852_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572
Processed 147000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2344:12289:26116_1:N:0:GTCGGAGC+TTATAACC ptg000109l 39606
Processed 148000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2348:14166:8830_1:N:0:GTCGGAGC+TTATAACC ptg000092l 1
Processed 149000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2350:48251:24379_1:N:0:ATCGGAGC+TTATAACC ptg000033l 2625572
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2351:8032:27657_1:N:0:GTCGGAGC+TTATAACC ptg000128l 1
Processed 150000000 sequence pairs so far
Processed 151000000 sequence pairs so far
Processed 152000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2366:44140:3059_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625624
Processed 153000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2368:22687:16997_1:N:0:GTCGGAGC+TTATAACC ptg000069l 259768
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2368:22695:17011_1:N:0:GTCGGAGC+TTATAACC ptg000069l 259768
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2369:51423:3844_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2369:50767:19546_1:N:0:GTCGGAGC+TTATAACC ptg000109l 39590
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2370:27494:9825_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625572
Processed 154000000 sequence pairs so far
Processed 155000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2376:9675:27307_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625624
Processed 156000000 sequence pairs so far
Processed 157000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2387:46486:27405_1:N:0:GTCGGAGC+TTATAACC ptg000018l 3
Processed 158000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2392:41453:4012_1:N:0:GTCGGAGC+TTATAACC ptg000109l 39589
Processed 159000000 sequence pairs so far
Processed 160000000 sequence pairs so far
Processed 161000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2407:10638:15610_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625665
Processed 162000000 sequence pairs so far
Processed 163000000 sequence pairs so far
Processed 164000000 sequence pairs so far
Processed 165000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2427:14603:13061_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625589
Processed 166000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2432:38710:13719_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625609
Processed 167000000 sequence pairs so far
182967324 reads; of these:
182967324 (100.00%) were paired; of these:
137379430 (75.08%) aligned concordantly 0 times
14799364 (8.09%) aligned concordantly exactly 1 time
30788530 (16.83%) aligned concordantly >1 times
24.92% overall alignment rate
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2436:4059:22880_1:N:0:GTCGGAGC+TTATAACC ptg000109l 39659
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2437:4577:20639_1:N:0:GTCGGAGC+TTATAACC ptg000061l 1
Processed 168000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2440:40053:25149_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625571
Processed 169000000 sequence pairs so far
182967324 reads; of these:
182967324 (100.00%) were paired; of these:
122405770 (66.90%) aligned concordantly 0 times
19413525 (10.61%) aligned concordantly exactly 1 time
41148029 (22.49%) aligned concordantly >1 times
33.10% overall alignment rate
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2446:50589:13075_1:N:0:GTCGGAGC+TTATAACC ptg000109l 39607
Processed 170000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2449:44828:7444_1:N:0:GTCGGAGC+TTATAACC ptg000074l 12210
Processed 171000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2453:34801:14237_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625634
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2453:50233:25037_1:N:0:GTCGGAGC+TTATAACC ptg000109l 39607
Processed 172000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2457:47652:14882_1:N:0:GTCGGAGC+TTATAACC ptg000069l 259768
Processed 173000000 sequence pairs so far
182967324 reads; of these:
182967324 (100.00%) were paired; of these:
137414901 (75.10%) aligned concordantly 0 times
14786659 (8.08%) aligned concordantly exactly 1 time
30765764 (16.81%) aligned concordantly >1 times
24.90% overall alignment rate
Processed 174000000 sequence pairs so far
Processed 175000000 sequence pairs so far
182967324 reads; of these:
182967324 (100.00%) were paired; of these:
122402919 (66.90%) aligned concordantly 0 times
19439080 (10.62%) aligned concordantly exactly 1 time
41125325 (22.48%) aligned concordantly >1 times
33.10% overall alignment rate
Processed 176000000 sequence pairs so far
Processed 177000000 sequence pairs so far
Processed 178000000 sequence pairs so far
Processed 179000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2485:44285:29310_1:N:0:GTCGGAGC+TTATAACC ptg000026l 1
Processed 180000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2486:17638:8956_1:N:0:GTCGGAGC+TTATAACC ptg000122l 1
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2487:13260:14630_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625577
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2487:37998:14812_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625667
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2488:16828:4782_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625613
Processed 181000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2490:30132:19630_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625575
Processed 182000000 sequence pairs so far
Chromosomal sequence could not be extracted for LH00260:131:22L7V3LT4:3:2495:47101:19056_1:N:0:GTCGGAGC+TTATAACC ptg000033l 2625575
Processed 182967324 sequences in total
Successfully deleted the temporary files trimmed_ACR-178-TP2_S1_R1_001.fastq.gz_C_to_T.fastq, trimmed_ACR-178-TP2_S1_R1_001.fastq.gz_G_to_A.fastq, trimmed_ACR-178-TP2_S1_R2_001.fastq.gz_C_to_T.fastq and trimmed_ACR-178-TP2_S1_R2_001.fastq.gz_G_to_A.fastq
Final Alignment report
======================
Sequence pairs analysed in total: 182967324
Final Cytosine Methylation Report
=================================
Total number of C's analysed: 3994751719
Total methylated C's in CpG context: 70399594
Total methylated C's in CHG context: 12957412
Total methylated C's in CHH context: 62458470
Total methylated C's in Unknown context: 11680962
Total unmethylated C's in CpG context: 629501595
Total unmethylated C's in CHG context: 739934104
Total unmethylated C's in CHH context: 2479500544
Total unmethylated C's in Unknown context: 43368441
C methylated in CpG context: 10.1%
C methylated in CHG context: 1.7%
C methylated in CHH context: 2.5%
C methylated in unknown context (CN or CHN): 21.2%
Bismark completed in 1d 1h 6m 22s
====================
Bismark run complete
====================