BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089708.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 20,895,852 number of mapped reads = 19,439,099 (93.03%) number of supplementary alignments = 99,632 (0.48%) number of secondary alignments = 0 number of mapped bases = 1,253,993,119 bp number of sequenced bases = 1,253,528,796 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,451,870 duplication rate = 17.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6843 >>>>>>> ACTG content number of A's = 319,975,271 bp (25.53%) number of C's = 228,665,750 bp (18.24%) number of T's = 397,389,640 bp (31.7%) number of G's = 307,443,210 bp (24.53%) number of N's = 54,925 bp (0%) GC percentage = 42.77% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 7,777,172 number of insertions = 84,765 mapped reads with insertion percentage = 0.43% number of deletions = 265,211 mapped reads with deletion percentage = 1.35% homopolymer indels = 47.88% >>>>>>> Coverage mean coverageData = 0.4051X std coverageData = 2.4965X There is a 13.59% of reference with a coverageData >= 1X There is a 7.93% of reference with a coverageData >= 2X There is a 5.15% of reference with a coverageData >= 3X There is a 3.5% of reference with a coverageData >= 4X There is a 2.44% of reference with a coverageData >= 5X There is a 1.74% of reference with a coverageData >= 6X There is a 1.26% of reference with a coverageData >= 7X There is a 0.93% of reference with a coverageData >= 8X There is a 0.7% of reference with a coverageData >= 9X There is a 0.53% of reference with a coverageData >= 10X There is a 0.41% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.25% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% 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 97501226 0.3911774647093056 4.2137699466182355 chr2 243199373 108934723 0.4479235355594441 3.0198312790247748 chr3 198022430 86866096 0.4386679630181288 1.6250770394277736 chr4 191154276 82141408 0.42971263692788125 1.8938078902990407 chr5 180915260 78854574 0.4358646915688594 1.596003064783166 chr6 171115067 73577920 0.4299908902820346 2.2897588701666765 chr7 159138663 66103231 0.41538133948002315 2.7681838870173943 chr8 146364022 66148296 0.4519436887297344 3.068307894564185 chr9 141213431 52123832 0.3691138415863573 2.19894626048146 chr10 135534747 55782299 0.411571941769294 2.786057230554851 chr11 135006516 55841639 0.41362180622452327 2.0473876291356357 chr12 133851895 59107792 0.44159099876770513 1.9461197313667629 chr13 115169878 39133210 0.3397868494746517 1.3855887549134331 chr14 107349540 39003677 0.3633334339392605 1.6165650237087474 chr15 102531392 34804063 0.33944787368145746 1.8724473087957236 chr16 90354753 36405041 0.4029122961577904 1.8318091265036829 chr17 81195210 34276493 0.4221492006732909 1.9551856576872724 chr18 78077248 32103239 0.4111727785282596 4.607689827105557 chr19 59128983 23734126 0.4013958095643214 2.6794119248670762 chr20 63025520 27522286 0.43668479054199 1.7702046862506937 chr21 48129895 16382582 0.3403826665318925 1.9175958605852017 chr22 51304566 13577596 0.2646469322048256 1.264939754437304 chrMT 16571 24763 1.49435761269688 2.2610428228690744 chrX 155270560 70628334 0.45487266871453286 1.865019347369825 chrY 59373566 3414673 0.057511671102928194 1.3811748089312401