BamQC report ----------------------------------- >>>>>>> Input bam file = SRR961011.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 385,800,550 number of mapped reads = 366,065,892 (94.88%) number of supplementary alignments = 5,941,743 (1.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 188,759,704 number of mapped paired reads (second in pair) = 177,306,188 number of mapped paired reads (both in pair) = 353,505,484 number of mapped paired reads (singletons) = 12,560,408 number of mapped bases = 35,797,567,546 bp number of sequenced bases = 35,787,381,272 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,834,830 duplication rate = 10.92% >>>>>>> Insert size mean insert size = 85,434.3734 std insert size = 2,817,553.9187 median insert size = 142 >>>>>>> Mapping quality mean mapping quality = 53.11 >>>>>>> ACTG content number of A's = 10,402,571,013 bp (29.07%) number of C's = 7,374,863,386 bp (20.61%) number of T's = 10,355,248,419 bp (28.94%) number of G's = 7,451,406,022 bp (20.82%) number of N's = 203,292,432 bp (0.57%) GC percentage = 41.43% >>>>>>> Mismatches and indels general error rate = 0.0164 number of mismatches = 576,494,259 number of insertions = 3,594,593 mapped reads with insertion percentage = 0.95% number of deletions = 4,196,489 mapped reads with deletion percentage = 1.11% homopolymer indels = 39.97% >>>>>>> Coverage mean coverageData = 11.5637X std coverageData = 140.3108X There is a 91.27% of reference with a coverageData >= 1X There is a 90.38% of reference with a coverageData >= 2X There is a 88.76% of reference with a coverageData >= 3X There is a 86.32% of reference with a coverageData >= 4X There is a 82.94% of reference with a coverageData >= 5X There is a 78.68% of reference with a coverageData >= 6X There is a 73.63% of reference with a coverageData >= 7X There is a 67.96% of reference with a coverageData >= 8X There is a 61.87% of reference with a coverageData >= 9X There is a 55.6% of reference with a coverageData >= 10X There is a 49.33% of reference with a coverageData >= 11X There is a 43.25% of reference with a coverageData >= 12X There is a 37.49% of reference with a coverageData >= 13X There is a 32.16% of reference with a coverageData >= 14X There is a 27.32% of reference with a coverageData >= 15X There is a 23% of reference with a coverageData >= 16X There is a 19.21% of reference with a coverageData >= 17X There is a 15.94% of reference with a coverageData >= 18X There is a 13.13% of reference with a coverageData >= 19X There is a 10.77% of reference with a coverageData >= 20X There is a 8.79% of reference with a coverageData >= 21X There is a 7.15% of reference with a coverageData >= 22X There is a 5.81% of reference with a coverageData >= 23X There is a 4.71% of reference with a coverageData >= 24X There is a 3.82% of reference with a coverageData >= 25X There is a 3.1% of reference with a coverageData >= 26X There is a 2.52% of reference with a coverageData >= 27X There is a 2.05% of reference with a coverageData >= 28X There is a 1.68% of reference with a coverageData >= 29X There is a 1.38% of reference with a coverageData >= 30X There is a 1.14% of reference with a coverageData >= 31X There is a 0.95% of reference with a coverageData >= 32X There is a 0.8% of reference with a coverageData >= 33X There is a 0.68% of reference with a coverageData >= 34X There is a 0.58% of reference with a coverageData >= 35X There is a 0.5% of reference with a coverageData >= 36X There is a 0.44% of reference with a coverageData >= 37X There is a 0.39% of reference with a coverageData >= 38X There is a 0.35% of reference with a coverageData >= 39X There is a 0.31% of reference with a coverageData >= 40X There is a 0.29% of reference with a coverageData >= 41X There is a 0.26% of reference with a coverageData >= 42X There is a 0.24% of reference with a coverageData >= 43X There is a 0.23% of reference with a coverageData >= 44X There is a 0.21% of reference with a coverageData >= 45X There is a 0.2% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3311940591 13.287592134023209 360.7475105006439 chr2 243199373 3022941526 12.429890294166178 82.09672496366171 chr3 198022430 2426329040 12.252799038977555 30.86665675513549 chr4 191154276 2140957518 11.200154988947252 91.32539302196069 chr5 180915260 1722816272 9.522780289512339 13.862239653912493 chr6 171115067 1759396695 10.281950770588775 44.096052923444574 chr7 159138663 2023026727 12.712352164225484 90.2744971900463 chr8 146364022 1840160880 12.572494625762607 117.09857376330876 chr9 141213431 1701586935 12.049752795822942 105.62974773130195 chr10 135534747 1772219754 13.075759487712771 307.83772355108005 chr11 135006516 1624777397 12.034807245896191 59.00994630222625 chr12 133851895 1345151428 10.049550871132606 11.796879407071836 chr13 115169878 1096599531 9.521582813520043 6.995692403067955 chr14 107349540 787677985 7.337506849121104 11.39082099056927 chr15 102531392 945915518 9.225618608591601 7.115139152975896 chr16 90354753 1332443014 14.746794936177846 148.36409778513956 chr17 81195210 763153469 9.398996184627148 35.33609797996408 chr18 78077248 1361426340 17.436915040857997 133.735644375707 chr19 59128983 790570054 13.370263006214735 174.91473681826022 chr20 63025520 698140693 11.077111192418563 33.77184695835546 chr21 48129895 500447156 10.397844333547788 51.53390651003257 chr22 51304566 412777346 8.045625919533165 9.280916976426054 chrMT 16571 8090534 488.234506064812 89.33649310822719 chrX 155270560 2288342739 14.73777604073818 45.761902117642684 chrY 59373566 120678404 2.032527471905595 103.41223023212909