BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514704.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 40,964,776 number of mapped reads = 40,599,449 (99.11%) number of supplementary alignments = 1,972,695 (4.82%) number of secondary alignments = 0 number of mapped bases = 3,853,193,505 bp number of sequenced bases = 3,850,268,609 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,381,213 duplication rate = 37.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 31.4223 >>>>>>> ACTG content number of A's = 1,133,994,585 bp (29.45%) number of C's = 789,638,489 bp (20.51%) number of T's = 1,118,868,266 bp (29.06%) number of G's = 798,613,470 bp (20.74%) number of N's = 9,153,799 bp (0.24%) GC percentage = 41.25% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 23,825,624 number of insertions = 1,317,794 mapped reads with insertion percentage = 3.14% number of deletions = 1,338,143 mapped reads with deletion percentage = 3.17% homopolymer indels = 42.01% >>>>>>> Coverage mean coverageData = 1.2447X std coverageData = 85.1116X There is a 5.59% of reference with a coverageData >= 1X There is a 3.9% of reference with a coverageData >= 2X There is a 3.29% of reference with a coverageData >= 3X There is a 2.96% of reference with a coverageData >= 4X There is a 2.72% of reference with a coverageData >= 5X There is a 2.53% of reference with a coverageData >= 6X There is a 2.37% of reference with a coverageData >= 7X There is a 2.23% of reference with a coverageData >= 8X There is a 2.12% of reference with a coverageData >= 9X There is a 2.01% of reference with a coverageData >= 10X There is a 1.91% of reference with a coverageData >= 11X There is a 1.82% of reference with a coverageData >= 12X There is a 1.74% of reference with a coverageData >= 13X There is a 1.67% of reference with a coverageData >= 14X There is a 1.6% of reference with a coverageData >= 15X There is a 1.54% of reference with a coverageData >= 16X There is a 1.48% of reference with a coverageData >= 17X There is a 1.42% of reference with a coverageData >= 18X There is a 1.37% of reference with a coverageData >= 19X There is a 1.32% of reference with a coverageData >= 20X There is a 1.28% of reference with a coverageData >= 21X There is a 1.23% of reference with a coverageData >= 22X There is a 1.19% of reference with a coverageData >= 23X There is a 1.15% of reference with a coverageData >= 24X There is a 1.11% of reference with a coverageData >= 25X There is a 1.08% of reference with a coverageData >= 26X There is a 1.05% of reference with a coverageData >= 27X There is a 1.02% of reference with a coverageData >= 28X There is a 0.99% of reference with a coverageData >= 29X There is a 0.96% of reference with a coverageData >= 30X There is a 0.93% of reference with a coverageData >= 31X There is a 0.9% of reference with a coverageData >= 32X There is a 0.88% of reference with a coverageData >= 33X There is a 0.85% of reference with a coverageData >= 34X There is a 0.83% of reference with a coverageData >= 35X There is a 0.81% of reference with a coverageData >= 36X There is a 0.79% of reference with a coverageData >= 37X There is a 0.77% of reference with a coverageData >= 38X There is a 0.75% of reference with a coverageData >= 39X There is a 0.73% of reference with a coverageData >= 40X There is a 0.71% of reference with a coverageData >= 41X There is a 0.69% of reference with a coverageData >= 42X There is a 0.68% of reference with a coverageData >= 43X There is a 0.66% of reference with a coverageData >= 44X There is a 0.64% of reference with a coverageData >= 45X There is a 0.63% of reference with a coverageData >= 46X There is a 0.61% of reference with a coverageData >= 47X There is a 0.6% of reference with a coverageData >= 48X There is a 0.59% of reference with a coverageData >= 49X There is a 0.57% of reference with a coverageData >= 50X There is a 0.56% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 519962628 2.0861036410416807 35.152660055091296 chr2 243199373 446873583 1.8374783515580857 37.814799031101714 chr3 198022430 530725694 2.6801291853655163 193.4972441264369 chr4 191154276 310401507 1.6238271698405533 22.151928410109907 chr5 180915260 408508467 2.258010004241765 19.66724828432611 chr6 171115067 364711086 2.1313791496806065 227.11262894233425 chr7 159138663 338240569 2.1254455870349998 25.4692230336589 chr8 146364022 231336486 1.5805556778154128 21.525593568914083 chr9 141213431 405066475 2.8684698907995516 189.863507278595 chr10 135534747 180018418 1.3282086105934148 22.256976560241526 chr11 135006516 100335745 0.7431918693465136 14.960313515427163 chr12 133851895 2015379 0.015056783469520548 0.35680888247589015 chr13 115169878 1240925 0.010774735734286356 0.848422690647873 chr14 107349540 1287283 0.011991509232363735 0.5407958400193763 chr15 102531392 1448472 0.014127107530150377 0.900913750769589 chr16 90354753 1213716 0.013432785323423993 0.43633298188008107 chr17 81195210 1128711 0.013901201807347994 0.4934174392063677 chr18 78077248 979051 0.012539517273969493 0.2709052053597081 chr19 59128983 1603959 0.027126443219901143 2.085003592887934 chr20 63025520 1306906 0.020736139900154733 6.258779664397339 chr21 48129895 923925 0.01919648900127457 0.5725974688736944 chr22 51304566 542508 0.010574263507072645 0.9447467059428408 chrMT 16571 139387 8.411502021604006 24.682219688139895 chrX 155270560 2710804 0.017458583262660997 0.34888613204181446 chrY 59373566 471821 0.007946650871534311 0.3417614943513271