BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514757.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 = 55,550,737 number of mapped reads = 52,026,322 (93.66%) number of supplementary alignments = 8,084,784 (14.55%) number of secondary alignments = 0 number of mapped bases = 4,924,558,436 bp number of sequenced bases = 4,920,729,407 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,938,534 duplication rate = 44.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1768 >>>>>>> ACTG content number of A's = 1,531,066,006 bp (31.11%) number of C's = 908,489,377 bp (18.46%) number of T's = 1,526,708,693 bp (31.03%) number of G's = 954,129,163 bp (19.39%) number of N's = 336,168 bp (0.01%) GC percentage = 37.85% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 25,939,083 number of insertions = 3,309,633 mapped reads with insertion percentage = 6.09% number of deletions = 1,339,416 mapped reads with deletion percentage = 2.42% homopolymer indels = 49.85% >>>>>>> Coverage mean coverageData = 1.5908X std coverageData = 86.4841X There is a 5.12% of reference with a coverageData >= 1X There is a 3.41% of reference with a coverageData >= 2X There is a 2.79% of reference with a coverageData >= 3X There is a 2.44% of reference with a coverageData >= 4X There is a 2.21% of reference with a coverageData >= 5X There is a 2.03% of reference with a coverageData >= 6X There is a 1.89% of reference with a coverageData >= 7X There is a 1.78% of reference with a coverageData >= 8X There is a 1.68% of reference with a coverageData >= 9X There is a 1.59% of reference with a coverageData >= 10X There is a 1.52% of reference with a coverageData >= 11X There is a 1.45% of reference with a coverageData >= 12X There is a 1.4% of reference with a coverageData >= 13X There is a 1.34% of reference with a coverageData >= 14X There is a 1.29% of reference with a coverageData >= 15X There is a 1.25% of reference with a coverageData >= 16X There is a 1.21% of reference with a coverageData >= 17X There is a 1.17% of reference with a coverageData >= 18X There is a 1.13% of reference with a coverageData >= 19X There is a 1.1% of reference with a coverageData >= 20X There is a 1.07% of reference with a coverageData >= 21X There is a 1.04% of reference with a coverageData >= 22X There is a 1.01% of reference with a coverageData >= 23X There is a 0.99% of reference with a coverageData >= 24X There is a 0.96% of reference with a coverageData >= 25X There is a 0.94% of reference with a coverageData >= 26X There is a 0.92% of reference with a coverageData >= 27X There is a 0.9% of reference with a coverageData >= 28X There is a 0.88% of reference with a coverageData >= 29X There is a 0.86% of reference with a coverageData >= 30X There is a 0.84% of reference with a coverageData >= 31X There is a 0.82% of reference with a coverageData >= 32X There is a 0.8% of reference with a coverageData >= 33X There is a 0.79% of reference with a coverageData >= 34X There is a 0.77% of reference with a coverageData >= 35X There is a 0.76% of reference with a coverageData >= 36X There is a 0.74% of reference with a coverageData >= 37X There is a 0.73% of reference with a coverageData >= 38X There is a 0.72% of reference with a coverageData >= 39X There is a 0.7% of reference with a coverageData >= 40X There is a 0.69% of reference with a coverageData >= 41X There is a 0.68% of reference with a coverageData >= 42X There is a 0.67% of reference with a coverageData >= 43X There is a 0.65% 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 0.62% of reference with a coverageData >= 47X There is a 0.61% of reference with a coverageData >= 48X There is a 0.6% of reference with a coverageData >= 49X There is a 0.59% of reference with a coverageData >= 50X There is a 0.59% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 396233339 1.5896985026970103 29.735226745776853 chr2 243199373 418936108 1.722603569376801 67.03046679827112 chr3 198022430 526834915 2.660481012176247 224.9196897049819 chr4 191154276 292666806 1.531050270620156 38.31556746933634 chr5 180915260 202873332 1.1213721385360196 19.217729763551613 chr6 171115067 331320422 1.936243416834825 93.3612559208169 chr7 159138663 225333736 1.4159584588190237 56.154499397929534 chr8 146364022 192898151 1.3179342051696283 21.794974460498153 chr9 141213431 274257499 1.9421488243565161 196.36413033109497 chr10 135534747 200241724 1.477419838323821 24.307604626185523 chr11 135006516 216028199 1.6001316484605825 26.9261400935461 chr12 133851895 228109923 1.7041964404015348 23.51801584845071 chr13 115169878 217465019 1.8882109000757994 49.103871723042246 chr14 107349540 206567411 1.9242505463926534 49.2748948287851 chr15 102531392 76365646 0.7448025868994347 16.745608562681458 chr16 90354753 54922613 0.6078552724282252 14.424970035030924 chr17 81195210 45044932 0.5547732680289884 14.312125003848184 chr18 78077248 167888866 2.1502917981945266 25.03146879151747 chr19 59128983 38011810 0.6428625704588898 12.229400590386671 chr20 63025520 97374916 1.5450077365486234 36.47594824355341 chr21 48129895 43297980 0.8996067828529442 15.457197641597798 chr22 51304566 36821195 0.7176982064325425 82.53677658367562 chrMT 16571 128861136 7776.304145796874 6557.303131571476 chrX 155270560 203290331 1.3092651369325905 23.97065173261219 chrY 59373566 102912427 1.7333037904443873 116.59896137046246