BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514750.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 = 56,341,149 number of mapped reads = 52,666,195 (93.48%) number of supplementary alignments = 7,915,099 (14.05%) number of secondary alignments = 0 number of mapped bases = 4,999,041,112 bp number of sequenced bases = 4,995,156,822 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,087,760 duplication rate = 43.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4434 >>>>>>> ACTG content number of A's = 1,544,489,747 bp (30.92%) number of C's = 934,263,913 bp (18.7%) number of T's = 1,533,444,166 bp (30.7%) number of G's = 982,613,274 bp (19.67%) number of N's = 345,722 bp (0.01%) GC percentage = 38.37% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 27,664,980 number of insertions = 3,569,848 mapped reads with insertion percentage = 6.49% number of deletions = 1,328,896 mapped reads with deletion percentage = 2.37% homopolymer indels = 52.19% >>>>>>> Coverage mean coverageData = 1.6148X std coverageData = 82.8039X There is a 5.45% of reference with a coverageData >= 1X There is a 3.6% of reference with a coverageData >= 2X There is a 2.92% of reference with a coverageData >= 3X There is a 2.54% of reference with a coverageData >= 4X There is a 2.29% of reference with a coverageData >= 5X There is a 2.1% of reference with a coverageData >= 6X There is a 1.95% of reference with a coverageData >= 7X There is a 1.82% of reference with a coverageData >= 8X There is a 1.72% of reference with a coverageData >= 9X There is a 1.63% of reference with a coverageData >= 10X There is a 1.55% of reference with a coverageData >= 11X There is a 1.48% of reference with a coverageData >= 12X There is a 1.42% of reference with a coverageData >= 13X There is a 1.36% of reference with a coverageData >= 14X There is a 1.31% of reference with a coverageData >= 15X There is a 1.26% of reference with a coverageData >= 16X There is a 1.22% of reference with a coverageData >= 17X There is a 1.18% of reference with a coverageData >= 18X There is a 1.14% of reference with a coverageData >= 19X There is a 1.11% of reference with a coverageData >= 20X There is a 1.08% of reference with a coverageData >= 21X There is a 1.05% of reference with a coverageData >= 22X There is a 1.02% of reference with a coverageData >= 23X There is a 0.99% of reference with a coverageData >= 24X There is a 0.97% 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 400099032 1.6052077639557816 52.99545415924821 chr2 243199373 348960852 1.4348756236308224 23.64419411735467 chr3 198022430 392929784 1.9842690749729714 46.798008194721305 chr4 191154276 423165598 2.213738593009554 31.765904639049754 chr5 180915260 426471355 2.3572989641669806 31.668914127337587 chr6 171115067 227545351 1.329779749903613 25.716826342010048 chr7 159138663 243466528 1.5299018064516479 40.18406082419097 chr8 146364022 244735825 1.672103715488223 111.13205551019327 chr9 141213431 156937972 1.1113530128731168 43.83070468937002 chr10 135534747 175850146 1.2974543420957578 41.318547824865064 chr11 135006516 298426623 2.210460886199004 32.77758197754453 chr12 133851895 225704108 1.6862227314749634 51.010369482033845 chr13 115169878 146360913 1.2708263266546136 21.152734118930415 chr14 107349540 327111457 3.047162167625497 367.4160817673247 chr15 102531392 127436392 1.2429012179996541 22.517986668526444 chr16 90354753 85316679 0.9442411845229658 16.06480585689225 chr17 81195210 113431022 1.3970161786637414 23.67207746657673 chr18 78077248 154461418 1.9783153473851947 65.58123329619274 chr19 59128983 74596143 1.2615833930375566 76.2662823665678 chr20 63025520 80603710 1.278905909860006 28.53342677761371 chr21 48129895 68723205 1.4278694146330466 23.645013494020525 chr22 51304566 49184737 0.9586814748613213 54.18780094643032 chrMT 16571 79563327 4801.359423088528 4960.033251366864 chrX 155270560 92227562 0.5939797087097516 15.086452744940576 chrY 59373566 35731373 0.601806079830206 12.850233871058554