BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082498.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,926,882 number of mapped reads = 2,651,776 (90.6%) number of supplementary alignments = 27,560 (0.94%) number of secondary alignments = 0 number of mapped bases = 179,288,268 bp number of sequenced bases = 179,219,800 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 129,583 duplication rate = 3.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.958 >>>>>>> ACTG content number of A's = 50,721,897 bp (28.3%) number of C's = 33,942,379 bp (18.94%) number of T's = 55,655,227 bp (31.05%) number of G's = 38,896,507 bp (21.7%) number of N's = 3,790 bp (0%) GC percentage = 40.64% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,484,777 number of insertions = 14,131 mapped reads with insertion percentage = 0.53% number of deletions = 42,553 mapped reads with deletion percentage = 1.59% homopolymer indels = 47.19% >>>>>>> Coverage mean coverageData = 0.0579X std coverageData = 0.4533X There is a 4.65% of reference with a coverageData >= 1X There is a 0.82% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% 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 14246190 0.05715608628313107 0.7675176750200716 chr2 243199373 14002309 0.05757543215376629 0.5066487767942274 chr3 198022430 11567350 0.05841434225405678 0.2892087910872576 chr4 191154276 11074728 0.057936072536509724 0.30168826219510836 chr5 180915260 12265592 0.06779744284699919 0.311170968960567 chr6 171115067 12508539 0.0731001613084136 0.46880499097164335 chr7 159138663 11435372 0.07185791173826815 0.4773138073503868 chr8 146364022 9619120 0.06572052249288421 0.8219641731486375 chr9 141213431 7553323 0.053488701085380466 0.36842400443805495 chr10 135534747 8465914 0.062463052371359795 0.39660859710093754 chr11 135006516 6797036 0.05034598478194934 0.4623029321639532 chr12 133851895 8969657 0.06701180435286329 0.31453209479929745 chr13 115169878 4716438 0.040952010038597074 0.24259969179300864 chr14 107349540 3952593 0.03681984105381355 0.2560276143116005 chr15 102531392 5516769 0.053805657880856624 0.28328741915203365 chr16 90354753 5143559 0.056926269279934834 0.2970701901795795 chr17 81195210 4060168 0.05000501876896433 0.31184079321743097 chr18 78077248 4173290 0.05345078248659584 0.5735231708617616 chr19 59128983 3430652 0.05801980392593595 0.5904909887711609 chr20 63025520 3144143 0.04988682362319264 0.27406088162709524 chr21 48129895 2230818 0.046349945288681804 0.27407567423638596 chr22 51304566 2023432 0.0394396085525799 0.2331110287731041 chrMT 16571 11596 0.6997767183634059 0.9953785032122279 chrX 155270560 11957256 0.07700916387498055 0.3857736925599172 chrY 59373566 422424 0.007114681304471421 0.13065119477197562