BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504700.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 = 346,652,634 number of mapped reads = 311,148,119 (89.76%) number of supplementary alignments = 1,607,148 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 156,583,709 number of mapped paired reads (second in pair) = 154,564,410 number of mapped paired reads (both in pair) = 306,789,720 number of mapped paired reads (singletons) = 4,358,399 number of mapped bases = 30,246,342,591 bp number of sequenced bases = 30,239,913,350 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,264,471 duplication rate = 17.47% >>>>>>> Insert size mean insert size = 29,889.9875 std insert size = 1,642,404.3604 median insert size = 436 >>>>>>> Mapping quality mean mapping quality = 53.9717 >>>>>>> ACTG content number of A's = 8,027,316,893 bp (26.55%) number of C's = 7,010,118,632 bp (23.18%) number of T's = 8,001,758,807 bp (26.46%) number of G's = 7,189,555,558 bp (23.78%) number of N's = 11,163,460 bp (0.04%) GC percentage = 46.96% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 215,475,815 number of insertions = 2,090,597 mapped reads with insertion percentage = 0.66% number of deletions = 2,604,679 mapped reads with deletion percentage = 0.81% homopolymer indels = 40.31% >>>>>>> Coverage mean coverageData = 9.7705X std coverageData = 19.9716X There is a 82.18% of reference with a coverageData >= 1X There is a 74.24% of reference with a coverageData >= 2X There is a 65.93% of reference with a coverageData >= 3X There is a 58.67% of reference with a coverageData >= 4X There is a 52.13% of reference with a coverageData >= 5X There is a 46.46% of reference with a coverageData >= 6X There is a 41.51% of reference with a coverageData >= 7X There is a 37.22% of reference with a coverageData >= 8X There is a 33.5% of reference with a coverageData >= 9X There is a 30.26% of reference with a coverageData >= 10X There is a 27.42% of reference with a coverageData >= 11X There is a 24.94% of reference with a coverageData >= 12X There is a 22.76% of reference with a coverageData >= 13X There is a 20.83% of reference with a coverageData >= 14X There is a 19.12% of reference with a coverageData >= 15X There is a 17.6% of reference with a coverageData >= 16X There is a 16.24% of reference with a coverageData >= 17X There is a 15.02% of reference with a coverageData >= 18X There is a 13.93% of reference with a coverageData >= 19X There is a 12.94% of reference with a coverageData >= 20X There is a 12.05% of reference with a coverageData >= 21X There is a 11.24% of reference with a coverageData >= 22X There is a 10.5% of reference with a coverageData >= 23X There is a 9.83% of reference with a coverageData >= 24X There is a 9.22% of reference with a coverageData >= 25X There is a 8.66% of reference with a coverageData >= 26X There is a 8.14% of reference with a coverageData >= 27X There is a 7.67% of reference with a coverageData >= 28X There is a 7.23% of reference with a coverageData >= 29X There is a 6.83% of reference with a coverageData >= 30X There is a 6.45% of reference with a coverageData >= 31X There is a 6.1% of reference with a coverageData >= 32X There is a 5.78% of reference with a coverageData >= 33X There is a 5.48% of reference with a coverageData >= 34X There is a 5.2% of reference with a coverageData >= 35X There is a 4.94% of reference with a coverageData >= 36X There is a 4.7% of reference with a coverageData >= 37X There is a 4.48% of reference with a coverageData >= 38X There is a 4.26% of reference with a coverageData >= 39X There is a 4.06% of reference with a coverageData >= 40X There is a 3.88% of reference with a coverageData >= 41X There is a 3.7% of reference with a coverageData >= 42X There is a 3.54% of reference with a coverageData >= 43X There is a 3.38% of reference with a coverageData >= 44X There is a 3.23% of reference with a coverageData >= 45X There is a 3.09% of reference with a coverageData >= 46X There is a 2.96% of reference with a coverageData >= 47X There is a 2.84% of reference with a coverageData >= 48X There is a 2.72% of reference with a coverageData >= 49X There is a 2.61% of reference with a coverageData >= 50X There is a 2.51% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2651555546 10.638110089202145 21.379303368317633 chr2 243199373 2009464742 8.262623037272386 13.2219908447704 chr3 198022430 1709529244 8.633008109232879 13.069006624566748 chr4 191154276 1398886600 7.31810257804539 12.56972779096684 chr5 180915260 2076737914 11.479064364166959 17.52067257494516 chr6 171115067 866626255 5.064581805645437 9.017450679314937 chr7 159138663 1429472731 8.982560894080152 13.536403656608917 chr8 146364022 1770504494 12.096582683413825 21.544623060096853 chr9 141213431 824033870 5.835378859961274 12.357572429906273 chr10 135534747 1795983401 13.251091994881579 19.771885944476317 chr11 135006516 1733061788 12.836875132752851 21.622549338002 chr12 133851895 1366386512 10.20819699265371 17.33351816888361 chr13 115169878 465355242 4.040598549561718 6.816828052266044 chr14 107349540 851382708 7.930939508450618 12.293249931087935 chr15 102531392 1224302569 11.940758289909885 19.21839531538521 chr16 90354753 1452155414 16.071710295085417 24.61913600375705 chr17 81195210 1040156946 12.810570303346712 20.630951141741505 chr18 78077248 558790564 7.156893695843378 58.28049497808214 chr19 59128983 1264569599 21.38662860140855 31.751407370542715 chr20 63025520 976611190 15.495488018186919 21.412890249118895 chr21 48129895 380063889 7.896628259837259 18.522081498302956 chr22 51304566 663444884 12.931497831986338 23.947647486219708 chrMT 16571 228437 13.78534789692837 5.999605055499977 chrX 155270560 1689515877 10.881108930115278 15.692515601634868 chrY 59373566 47522175 0.8003928044342157 27.701791253583263