BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514702.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 = 49,235,843 number of mapped reads = 48,829,934 (99.18%) number of supplementary alignments = 3,445,136 (7%) number of secondary alignments = 0 number of mapped bases = 4,619,778,061 bp number of sequenced bases = 4,609,123,221 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,193,270 duplication rate = 44.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.6364 >>>>>>> ACTG content number of A's = 1,320,091,926 bp (28.64%) number of C's = 982,667,429 bp (21.32%) number of T's = 1,307,951,538 bp (28.38%) number of G's = 994,673,337 bp (21.58%) number of N's = 3,738,991 bp (0.08%) GC percentage = 42.9% >>>>>>> Mismatches and indels general error rate = 0.0111 number of mismatches = 43,937,744 number of insertions = 3,140,794 mapped reads with insertion percentage = 5.97% number of deletions = 3,162,051 mapped reads with deletion percentage = 5.85% homopolymer indels = 26.19% >>>>>>> Coverage mean coverageData = 1.4923X std coverageData = 278.7715X There is a 4.52% of reference with a coverageData >= 1X There is a 2.57% of reference with a coverageData >= 2X There is a 1.89% of reference with a coverageData >= 3X There is a 1.59% of reference with a coverageData >= 4X There is a 1.4% of reference with a coverageData >= 5X There is a 1.27% of reference with a coverageData >= 6X There is a 1.17% of reference with a coverageData >= 7X There is a 1.09% of reference with a coverageData >= 8X There is a 1.02% of reference with a coverageData >= 9X There is a 0.97% of reference with a coverageData >= 10X There is a 0.92% of reference with a coverageData >= 11X There is a 0.88% of reference with a coverageData >= 12X There is a 0.84% of reference with a coverageData >= 13X There is a 0.81% of reference with a coverageData >= 14X There is a 0.78% of reference with a coverageData >= 15X There is a 0.75% of reference with a coverageData >= 16X There is a 0.73% of reference with a coverageData >= 17X There is a 0.71% of reference with a coverageData >= 18X There is a 0.68% of reference with a coverageData >= 19X There is a 0.67% of reference with a coverageData >= 20X There is a 0.65% of reference with a coverageData >= 21X There is a 0.63% of reference with a coverageData >= 22X There is a 0.61% of reference with a coverageData >= 23X There is a 0.6% of reference with a coverageData >= 24X There is a 0.58% of reference with a coverageData >= 25X There is a 0.57% of reference with a coverageData >= 26X There is a 0.56% of reference with a coverageData >= 27X There is a 0.55% of reference with a coverageData >= 28X There is a 0.53% of reference with a coverageData >= 29X There is a 0.52% of reference with a coverageData >= 30X There is a 0.51% of reference with a coverageData >= 31X There is a 0.5% of reference with a coverageData >= 32X There is a 0.49% of reference with a coverageData >= 33X There is a 0.48% of reference with a coverageData >= 34X There is a 0.47% of reference with a coverageData >= 35X There is a 0.47% of reference with a coverageData >= 36X There is a 0.46% of reference with a coverageData >= 37X There is a 0.45% of reference with a coverageData >= 38X There is a 0.44% of reference with a coverageData >= 39X There is a 0.43% of reference with a coverageData >= 40X There is a 0.43% of reference with a coverageData >= 41X There is a 0.42% of reference with a coverageData >= 42X There is a 0.41% of reference with a coverageData >= 43X There is a 0.41% of reference with a coverageData >= 44X There is a 0.4% of reference with a coverageData >= 45X There is a 0.4% of reference with a coverageData >= 46X There is a 0.39% of reference with a coverageData >= 47X There is a 0.38% of reference with a coverageData >= 48X There is a 0.38% of reference with a coverageData >= 49X There is a 0.37% of reference with a coverageData >= 50X There is a 0.37% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 294257825 1.180570077697018 32.37460980294626 chr2 243199373 854596856 3.513976394996709 754.2855292772665 chr3 198022430 198866489 1.0042624413810093 27.983303583669716 chr4 191154276 226782096 1.1863825426536627 31.048897787656472 chr5 180915260 335655627 1.8553195954835429 133.0336600923195 chr6 171115067 216739641 1.266630956583151 38.58990482126881 chr7 159138663 161785863 1.0166345497071319 32.4066611168642 chr8 146364022 216336858 1.4780740173975269 147.7355326430503 chr9 141213431 133163922 0.9429975679862916 27.150794516277358 chr10 135534747 189175582 1.3957718311157508 30.48107647207151 chr11 135006516 154262815 1.1426323674629157 21.877737055404413 chr12 133851895 359391471 2.684993522131308 380.67508218244956 chr13 115169878 369435969 3.2077482013135414 793.7949427322695 chr14 107349540 117466100 1.0942394350269222 28.65310950730685 chr15 102531392 91809773 0.8954308647248249 39.79371605443623 chr16 90354753 134350641 1.486923892094531 40.46850344006329 chr17 81195210 99562469 1.2262111151630743 25.822221099244675 chr18 78077248 105266037 1.3482293458908798 24.367991491319835 chr19 59128983 135878321 2.297998614317449 175.24502370971624 chr20 63025520 86265318 1.3687363150672933 29.208692564308418 chr21 48129895 31725184 0.6591575568573337 19.176818598866873 chr22 51304566 31630008 0.6165144833307818 33.56768642403981 chrMT 16571 1900936 114.7146219298775 167.6279062441672 chrX 155270560 61414240 0.3955304856245769 20.96663836915323 chrY 59373566 12058020 0.20308734698535708 15.551719982795847