BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971295.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 16,030,380 number of mapped reads = 13,814,785 (86.18%) number of secondary alignments = 0 number of mapped bases = 546,529,465 bp number of sequenced bases = 546,480,801 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,206,370 duplication rate = 7.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8535 >>>>>>> ACTG content number of A's = 159,399,271 bp (29.17%) number of C's = 110,996,493 bp (20.31%) number of T's = 162,002,602 bp (29.64%) number of G's = 114,072,915 bp (20.87%) number of N's = 9,520 bp (0%) GC percentage = 41.19% >>>>>>> Mismatches and indels general error rate = 0.0025 number of mismatches = 1,349,601 number of insertions = 14,718 mapped reads with insertion percentage = 0.11% number of deletions = 36,306 mapped reads with deletion percentage = 0.26% homopolymer indels = 41.55% >>>>>>> Coverage mean coverageData = 0.1765X std coverageData = 1.2738X There is a 11.45% of reference with a coverageData >= 1X There is a 3.71% of reference with a coverageData >= 2X There is a 1.31% of reference with a coverageData >= 3X There is a 0.5% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 42861276 0.17196055852554928 2.632549093434052 chr2 243199373 46139594 0.1897192144487971 0.9749465987359924 chr3 198022430 37430456 0.18902129420389396 0.6263402110861227 chr4 191154276 36476275 0.1908211302581586 0.7344966628284042 chr5 180915260 33879474 0.1872670884700384 0.6358830482642795 chr6 171115067 32782607 0.19158223512836542 0.7739832697204994 chr7 159138663 29832660 0.18746330676411427 1.5939989575779954 chr8 146364022 28124159 0.19215213285133692 2.335036359264707 chr9 141213431 22704384 0.16078062716286526 0.9177231775780024 chr10 135534747 25362032 0.18712568224294543 1.044213866812903 chr11 135006516 25045857 0.18551591243195995 1.0054109101243631 chr12 133851895 24409179 0.1823596072360425 0.6401230435467127 chr13 115169878 17556093 0.15243649906445156 0.5464987859983891 chr14 107349540 18735962 0.17453229888083358 0.7432626290993364 chr15 102531392 15395083 0.15014994627206465 0.551009206051863 chr16 90354753 14687859 0.16255767972715282 0.674173616133698 chr17 81195210 13340889 0.16430635501774057 0.690336189340614 chr18 78077248 14728505 0.18864016569846315 2.1934738032991077 chr19 59128983 9614420 0.162600801031873 2.209450723282685 chr20 63025520 10916901 0.1732139774491349 0.6384938229934408 chr21 48129895 6968409 0.14478338255256945 0.697354280646588 chr22 51304566 5682395 0.11075807560675983 0.46225277158924427 chrMT 16571 82536 4.980749502142297 5.536377411325755 chrX 155270560 31954610 0.2057995411364524 0.8069241305213704 chrY 59373566 1817850 0.03061716050540067 0.496630883141222