BamQC report ----------------------------------- >>>>>>> Input bam file = SRR630582.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 41,221,526 number of mapped reads = 40,274,612 (97.7%) number of supplementary alignments = 89,631 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 20,232,096 number of mapped paired reads (second in pair) = 20,042,516 number of mapped paired reads (both in pair) = 39,963,780 number of mapped paired reads (singletons) = 310,832 number of mapped bases = 3,904,043,286 bp number of sequenced bases = 3,901,227,688 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,924,688 duplication rate = 9.67% >>>>>>> Insert size mean insert size = 32,808.1752 std insert size = 1,817,808.1171 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 52.5922 >>>>>>> ACTG content number of A's = 1,141,368,351 bp (29.26%) number of C's = 776,413,276 bp (19.9%) number of T's = 1,153,013,821 bp (29.56%) number of G's = 829,852,944 bp (21.27%) number of N's = 579,296 bp (0.01%) GC percentage = 41.17% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 34,775,792 number of insertions = 709,427 mapped reads with insertion percentage = 1.73% number of deletions = 2,057,830 mapped reads with deletion percentage = 4.97% homopolymer indels = 54.05% >>>>>>> Coverage mean coverageData = 1.2611X std coverageData = 6.8912X There is a 22.46% of reference with a coverageData >= 1X There is a 15.72% of reference with a coverageData >= 2X There is a 11.81% of reference with a coverageData >= 3X There is a 9.37% of reference with a coverageData >= 4X There is a 7.66% of reference with a coverageData >= 5X There is a 6.4% of reference with a coverageData >= 6X There is a 5.42% of reference with a coverageData >= 7X There is a 4.65% of reference with a coverageData >= 8X There is a 4.03% of reference with a coverageData >= 9X There is a 3.52% of reference with a coverageData >= 10X There is a 3.09% of reference with a coverageData >= 11X There is a 2.73% of reference with a coverageData >= 12X There is a 2.42% of reference with a coverageData >= 13X There is a 2.16% of reference with a coverageData >= 14X There is a 1.93% of reference with a coverageData >= 15X There is a 1.74% of reference with a coverageData >= 16X There is a 1.56% of reference with a coverageData >= 17X There is a 1.41% of reference with a coverageData >= 18X There is a 1.28% of reference with a coverageData >= 19X There is a 1.16% of reference with a coverageData >= 20X There is a 1.06% of reference with a coverageData >= 21X There is a 0.96% of reference with a coverageData >= 22X There is a 0.88% of reference with a coverageData >= 23X There is a 0.8% of reference with a coverageData >= 24X There is a 0.74% of reference with a coverageData >= 25X There is a 0.68% of reference with a coverageData >= 26X There is a 0.62% of reference with a coverageData >= 27X There is a 0.57% of reference with a coverageData >= 28X There is a 0.53% of reference with a coverageData >= 29X There is a 0.49% of reference with a coverageData >= 30X There is a 0.45% of reference with a coverageData >= 31X There is a 0.42% of reference with a coverageData >= 32X There is a 0.39% of reference with a coverageData >= 33X There is a 0.36% of reference with a coverageData >= 34X There is a 0.33% of reference with a coverageData >= 35X There is a 0.31% of reference with a coverageData >= 36X There is a 0.29% of reference with a coverageData >= 37X There is a 0.27% of reference with a coverageData >= 38X There is a 0.25% of reference with a coverageData >= 39X There is a 0.23% of reference with a coverageData >= 40X There is a 0.22% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.12% of reference with a coverageData >= 50X There is a 0.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 339802364 1.3632959574451773 8.660145831359968 chr2 243199373 353346139 1.452907277848944 7.71241150479255 chr3 198022430 283603293 1.432177622504683 4.715387463614585 chr4 191154276 248670437 1.3008886968345923 5.676947728846844 chr5 180915260 251819526 1.3919197639823198 4.683408030915804 chr6 171115067 235903509 1.3786249985806334 5.489772076295514 chr7 159138663 207676572 1.3050038757709055 7.029019552779649 chr8 146364022 208365289 1.4236100248734624 4.831213425721534 chr9 141213431 174782207 1.2377165951020621 8.96000051286553 chr10 135534747 195810072 1.444722304310643 5.476403309511976 chr11 135006516 197671669 1.4641639148735606 7.801956082024965 chr12 133851895 187659254 1.4019917611177637 15.17681404836834 chr13 115169878 123322124 1.0707845327404097 4.105762616578202 chr14 107349540 127036429 1.1833905296659866 4.3476174985392975 chr15 102531392 123656709 1.2060375518943505 5.130600579143305 chr16 90354753 119256094 1.3198651984583478 6.688007106504348 chr17 81195210 104272847 1.284224118639511 5.105364668098672 chr18 78077248 110232946 1.4118446644021059 9.15944164825575 chr19 59128983 62361867 1.0546751159241146 6.027945622909891 chr20 63025520 98061229 1.5558971826015875 5.340397848236032 chr21 48129895 53199579 1.1053333692084721 5.44655709207431 chr22 51304566 48085991 0.937265330341163 4.0861829034419115 chrMT 16571 5103 0.3079476193349828 1.0211211930977033 chrX 155270560 7458221 0.048033709674261495 2.159185333151977 chrY 59373566 41983816 0.7071129263147172 5.493134157515526