BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153343.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 50,538,884 number of mapped reads = 50,040,083 (99.01%) number of supplementary alignments = 414,558 (0.82%) number of secondary alignments = 0 number of mapped bases = 4,861,852,207 bp number of sequenced bases = 4,860,982,636 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,088,613 duplication rate = 31.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.2156 >>>>>>> ACTG content number of A's = 1,295,705,292 bp (26.66%) number of C's = 1,128,487,481 bp (23.22%) number of T's = 1,321,041,054 bp (27.18%) number of G's = 1,113,947,400 bp (22.92%) number of N's = 1,801,409 bp (0.04%) GC percentage = 46.13% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 14,155,842 number of insertions = 523,568 mapped reads with insertion percentage = 1.03% number of deletions = 410,445 mapped reads with deletion percentage = 0.81% homopolymer indels = 49.08% >>>>>>> Coverage mean coverageData = 1.5705X std coverageData = 14.3566X There is a 23.43% of reference with a coverageData >= 1X There is a 11.86% of reference with a coverageData >= 2X There is a 6.58% of reference with a coverageData >= 3X There is a 4.82% of reference with a coverageData >= 4X There is a 3.82% of reference with a coverageData >= 5X There is a 3.3% of reference with a coverageData >= 6X There is a 2.95% of reference with a coverageData >= 7X There is a 2.7% of reference with a coverageData >= 8X There is a 2.5% of reference with a coverageData >= 9X There is a 2.34% of reference with a coverageData >= 10X There is a 2.21% of reference with a coverageData >= 11X There is a 2.09% of reference with a coverageData >= 12X There is a 1.98% of reference with a coverageData >= 13X There is a 1.89% of reference with a coverageData >= 14X There is a 1.8% of reference with a coverageData >= 15X There is a 1.72% of reference with a coverageData >= 16X There is a 1.65% of reference with a coverageData >= 17X There is a 1.59% of reference with a coverageData >= 18X There is a 1.52% of reference with a coverageData >= 19X There is a 1.47% of reference with a coverageData >= 20X There is a 1.41% of reference with a coverageData >= 21X There is a 1.36% of reference with a coverageData >= 22X There is a 1.32% of reference with a coverageData >= 23X There is a 1.27% of reference with a coverageData >= 24X There is a 1.23% of reference with a coverageData >= 25X There is a 1.19% of reference with a coverageData >= 26X There is a 1.15% of reference with a coverageData >= 27X There is a 1.12% of reference with a coverageData >= 28X There is a 1.09% of reference with a coverageData >= 29X There is a 1.05% of reference with a coverageData >= 30X There is a 1.02% of reference with a coverageData >= 31X There is a 0.99% of reference with a coverageData >= 32X There is a 0.97% of reference with a coverageData >= 33X There is a 0.94% of reference with a coverageData >= 34X There is a 0.91% of reference with a coverageData >= 35X There is a 0.89% of reference with a coverageData >= 36X There is a 0.87% of reference with a coverageData >= 37X There is a 0.84% of reference with a coverageData >= 38X There is a 0.82% of reference with a coverageData >= 39X There is a 0.8% of reference with a coverageData >= 40X There is a 0.78% of reference with a coverageData >= 41X There is a 0.76% of reference with a coverageData >= 42X There is a 0.75% of reference with a coverageData >= 43X There is a 0.73% of reference with a coverageData >= 44X There is a 0.71% of reference with a coverageData >= 45X There is a 0.69% of reference with a coverageData >= 46X There is a 0.68% of reference with a coverageData >= 47X There is a 0.66% of reference with a coverageData >= 48X There is a 0.65% of reference with a coverageData >= 49X There is a 0.63% of reference with a coverageData >= 50X There is a 0.62% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 555120692 2.22715871187338 24.471190864864674 chr2 243199373 344926349 1.418286341552369 11.174462966393293 chr3 198022430 248037732 1.25257392306518 9.444390365055915 chr4 191154276 186267726 0.9744366168403159 7.739993035026589 chr5 180915260 297063093 1.6420013049203257 13.55264914543641 chr6 171115067 164092493 0.9589599319152883 7.8836121995804875 chr7 159138663 226503622 1.4233098213223019 11.551896560986243 chr8 146364022 263542835 1.8005984763113438 19.22270830640664 chr9 141213431 123487061 0.8744710763383406 7.726016179677267 chr10 135534747 238339742 1.758513940340332 13.018093510056927 chr11 135006516 225108316 1.6673885281211167 12.242202397723903 chr12 133851895 237333743 1.77310708227179 13.085986549948505 chr13 115169878 59107641 0.5132213563688937 4.80570055827522 chr14 107349540 137956820 1.2851179427503834 10.38208661210778 chr15 102531392 228894146 2.2324299079056686 17.440563234179702 chr16 90354753 232302206 2.571001505587647 20.829134957669933 chr17 81195210 198946631 2.450226201767321 15.971343385947486 chr18 78077248 52645107 0.6742695003799314 5.685104832093471 chr19 59128983 252126072 4.264001496524978 25.68144896717303 chr20 63025520 117274933 1.860753120323323 14.73608073325189 chr21 48129895 53512677 1.111838639997033 10.99600745377468 chr22 51304566 63726105 1.2421137136215128 9.322148136045971 chrMT 16571 8399 0.5068493150684932 1.2748525125878711 chrX 155270560 351545790 2.264085284422237 20.138918836148477 chrY 59373566 3982276 0.0670715314623346 2.527318836215843