BamQC report ----------------------------------- >>>>>>> Input bam file = SRR961009.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 = 385,985,368 number of mapped reads = 368,532,445 (95.48%) number of supplementary alignments = 6,181,617 (1.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 189,822,048 number of mapped paired reads (second in pair) = 178,710,397 number of mapped paired reads (both in pair) = 356,481,622 number of mapped paired reads (singletons) = 12,050,823 number of mapped bases = 36,068,740,190 bp number of sequenced bases = 36,058,253,151 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,881,179 duplication rate = 11.01% >>>>>>> Insert size mean insert size = 86,098.0942 std insert size = 2,822,778.8919 median insert size = 142 >>>>>>> Mapping quality mean mapping quality = 53.0962 >>>>>>> ACTG content number of A's = 10,555,299,228 bp (29.27%) number of C's = 7,463,576,382 bp (20.7%) number of T's = 10,506,863,308 bp (29.14%) number of G's = 7,522,721,785 bp (20.86%) number of N's = 9,792,448 bp (0.03%) GC percentage = 41.56% >>>>>>> Mismatches and indels general error rate = 0.0116 number of mismatches = 406,623,002 number of insertions = 3,673,760 mapped reads with insertion percentage = 0.96% number of deletions = 4,307,653 mapped reads with deletion percentage = 1.13% homopolymer indels = 40.63% >>>>>>> Coverage mean coverageData = 11.6513X std coverageData = 144.0947X There is a 91.28% of reference with a coverageData >= 1X There is a 90.41% of reference with a coverageData >= 2X There is a 88.82% of reference with a coverageData >= 3X There is a 86.43% of reference with a coverageData >= 4X There is a 83.11% of reference with a coverageData >= 5X There is a 78.92% of reference with a coverageData >= 6X There is a 73.93% of reference with a coverageData >= 7X There is a 68.31% of reference with a coverageData >= 8X There is a 62.28% of reference with a coverageData >= 9X There is a 56.04% of reference with a coverageData >= 10X There is a 49.79% of reference with a coverageData >= 11X There is a 43.71% of reference with a coverageData >= 12X There is a 37.95% of reference with a coverageData >= 13X There is a 32.6% of reference with a coverageData >= 14X There is a 27.74% of reference with a coverageData >= 15X There is a 23.39% of reference with a coverageData >= 16X There is a 19.56% of reference with a coverageData >= 17X There is a 16.24% of reference with a coverageData >= 18X There is a 13.4% of reference with a coverageData >= 19X There is a 11% of reference with a coverageData >= 20X There is a 8.99% of reference with a coverageData >= 21X There is a 7.32% of reference with a coverageData >= 22X There is a 5.95% of reference with a coverageData >= 23X There is a 4.83% of reference with a coverageData >= 24X There is a 3.92% of reference with a coverageData >= 25X There is a 3.18% of reference with a coverageData >= 26X There is a 2.59% of reference with a coverageData >= 27X There is a 2.11% of reference with a coverageData >= 28X There is a 1.73% of reference with a coverageData >= 29X There is a 1.42% of reference with a coverageData >= 30X There is a 1.18% of reference with a coverageData >= 31X There is a 0.98% of reference with a coverageData >= 32X There is a 0.83% of reference with a coverageData >= 33X There is a 0.7% of reference with a coverageData >= 34X There is a 0.6% of reference with a coverageData >= 35X There is a 0.52% of reference with a coverageData >= 36X There is a 0.45% of reference with a coverageData >= 37X There is a 0.4% of reference with a coverageData >= 38X There is a 0.36% of reference with a coverageData >= 39X There is a 0.32% of reference with a coverageData >= 40X There is a 0.29% of reference with a coverageData >= 41X There is a 0.27% of reference with a coverageData >= 42X There is a 0.25% of reference with a coverageData >= 43X There is a 0.23% of reference with a coverageData >= 44X There is a 0.22% of reference with a coverageData >= 45X There is a 0.21% of reference with a coverageData >= 46X There is a 0.2% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3334839614 13.379463612249134 366.99896521178124 chr2 243199373 3049148022 12.537647545662052 85.16112638639434 chr3 198022430 2446081064 12.35254543639324 31.91299420693881 chr4 191154276 2161385143 11.307019587675873 97.05240791629294 chr5 180915260 1735938081 9.595310428760957 14.236550697463596 chr6 171115067 1773393229 10.36374680553408 44.78610562233087 chr7 159138663 2036492978 12.796971770461587 91.15140061400851 chr8 146364022 1854923442 12.673356584857991 127.5597639204039 chr9 141213431 1715381800 12.14744084788932 111.23313462422918 chr10 135534747 1788787461 13.197999041529918 317.7593787563426 chr11 135006516 1635063524 12.110997101799146 60.838594518813785 chr12 133851895 1353015592 10.108303599287854 12.108295271904842 chr13 115169878 1105175273 9.596044488299276 7.083229312234053 chr14 107349540 792826580 7.385467883700294 11.806007981976581 chr15 102531392 951501601 9.28010029357643 7.1660228130754176 chr16 90354753 1340340199 14.834196923763379 150.64399443114482 chr17 81195210 767401153 9.451310649975534 36.73879951469376 chr18 78077248 1374157440 17.599972785926063 139.58256983970932 chr19 59128983 793573470 13.42105731803302 179.07569668474636 chr20 63025520 701201459 11.125675107480271 34.854489947574116 chr21 48129895 505887384 10.510876535259426 53.26327637686584 chr22 51304566 413850042 8.066534311975273 9.455878570694438 chrMT 16571 8061690 486.49387484159075 83.90596997991179 chrX 155270560 2305949562 14.85117051165398 46.86376398393354 chrY 59373566 124364387 2.0946086849491237 110.13499699420755