BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472560.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 11,508,156 number of mapped reads = 11,326,217 (98.42%) number of supplementary alignments = 44,733 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,691,466 number of mapped paired reads (second in pair) = 5,634,751 number of mapped paired reads (both in pair) = 11,231,830 number of mapped paired reads (singletons) = 94,387 number of mapped bases = 1,111,428,066 bp number of sequenced bases = 1,111,293,749 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,725,815 duplication rate = 44.15% >>>>>>> Insert size mean insert size = 29,370.4601 std insert size = 1,665,450.0393 median insert size = 247 >>>>>>> Mapping quality mean mapping quality = 54.9112 >>>>>>> ACTG content number of A's = 308,530,375 bp (27.76%) number of C's = 248,943,932 bp (22.4%) number of T's = 305,908,045 bp (27.53%) number of G's = 247,742,748 bp (22.29%) number of N's = 168,649 bp (0.02%) GC percentage = 44.69% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 7,490,857 number of insertions = 60,341 mapped reads with insertion percentage = 0.53% number of deletions = 57,022 mapped reads with deletion percentage = 0.5% homopolymer indels = 45.51% >>>>>>> Coverage mean coverageData = 0.359X std coverageData = 14.5126X There is a 3.45% of reference with a coverageData >= 1X There is a 1.51% of reference with a coverageData >= 2X There is a 0.7% of reference with a coverageData >= 3X There is a 0.53% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.37% of reference with a coverageData >= 6X There is a 0.34% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.3% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.27% of reference with a coverageData >= 11X There is a 0.26% of reference with a coverageData >= 12X There is a 0.25% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.23% of reference with a coverageData >= 16X There is a 0.22% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.21% of reference with a coverageData >= 19X There is a 0.21% of reference with a coverageData >= 20X There is a 0.2% of reference with a coverageData >= 21X There is a 0.2% of reference with a coverageData >= 22X There is a 0.19% of reference with a coverageData >= 23X There is a 0.19% of reference with a coverageData >= 24X There is a 0.18% of reference with a coverageData >= 25X There is a 0.18% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.17% of reference with a coverageData >= 28X There is a 0.17% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.16% of reference with a coverageData >= 31X There is a 0.16% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.15% of reference with a coverageData >= 34X There is a 0.15% of reference with a coverageData >= 35X There is a 0.15% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.14% of reference with a coverageData >= 39X There is a 0.14% of reference with a coverageData >= 40X There is a 0.14% of reference with a coverageData >= 41X There is a 0.13% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.13% of reference with a coverageData >= 45X There is a 0.13% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.12% of reference with a coverageData >= 49X There is a 0.12% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 152369270 0.6113094899771584 24.485257081751868 chr2 243199373 55082731 0.226492076523569 6.9192309720817455 chr3 198022430 111998653 0.5655856914794956 14.24899775994803 chr4 191154276 51291775 0.26832658977505686 10.45755709427811 chr5 180915260 53305303 0.294642381189956 9.229363552217764 chr6 171115067 56468418 0.3300026057904065 10.22432786070837 chr7 159138663 57461513 0.36107826920727615 13.901760731491622 chr8 146364022 58763370 0.4014878055209497 15.659963168921008 chr9 141213431 61540069 0.4357947297520163 13.252381533839909 chr10 135534747 29187497 0.2153506583813522 9.03434171418776 chr11 135006516 61368521 0.45455969695566395 16.310752983686115 chr12 133851895 47655628 0.35603252385780565 13.658955957210466 chr13 115169878 23905975 0.20757141897814635 8.48935268482232 chr14 107349540 22378521 0.20846406048875477 7.858164519404654 chr15 102531392 33397154 0.3257261346846827 15.360312964605498 chr16 90354753 47861076 0.5297018077178519 17.166686942532007 chr17 81195210 41681781 0.513352708860535 13.03333688982387 chr18 78077248 15038436 0.1926097087848178 6.33074679334249 chr19 59128983 25349096 0.4287084727975112 17.89328260167415 chr20 63025520 15843600 0.25138388386164845 6.793424613294178 chr21 48129895 3556092 0.0738853055881381 3.0404409041113483 chr22 51304566 8185610 0.15954934693337042 4.621908734804241 chrMT 16571 2324 0.14024500633637077 0.44517614474225997 chrX 155270560 76574754 0.49316981918529823 28.596922107316836 chrY 59373566 1160899 0.019552455380564476 0.6025764024752931