BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618671.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 = 218,866,816 number of mapped reads = 211,990,830 (96.86%) number of supplementary alignments = 557,159 (0.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 105,977,378 number of mapped paired reads (second in pair) = 106,013,452 number of mapped paired reads (both in pair) = 209,102,344 number of mapped paired reads (singletons) = 2,888,486 number of mapped bases = 20,602,285,599 bp number of sequenced bases = 20,596,204,923 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,905,342 duplication rate = 12.03% >>>>>>> Insert size mean insert size = 42,150.4625 std insert size = 1,965,218.4915 median insert size = 256 >>>>>>> Mapping quality mean mapping quality = 53.6888 >>>>>>> ACTG content number of A's = 6,091,541,037 bp (29.58%) number of C's = 4,232,420,186 bp (20.55%) number of T's = 6,064,296,266 bp (29.44%) number of G's = 4,205,637,997 bp (20.42%) number of N's = 2,309,437 bp (0.01%) GC percentage = 40.97% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 209,334,740 number of insertions = 2,300,475 mapped reads with insertion percentage = 1.06% number of deletions = 2,628,068 mapped reads with deletion percentage = 1.21% homopolymer indels = 41.3% >>>>>>> Coverage mean coverageData = 6.6551X std coverageData = 62.9692X There is a 91.56% of reference with a coverageData >= 1X There is a 89.52% of reference with a coverageData >= 2X There is a 85.36% of reference with a coverageData >= 3X There is a 78.61% of reference with a coverageData >= 4X There is a 69.37% of reference with a coverageData >= 5X There is a 58.38% of reference with a coverageData >= 6X There is a 46.77% of reference with a coverageData >= 7X There is a 35.68% of reference with a coverageData >= 8X There is a 25.97% of reference with a coverageData >= 9X There is a 18.11% of reference with a coverageData >= 10X There is a 12.15% of reference with a coverageData >= 11X There is a 7.89% of reference with a coverageData >= 12X There is a 5% of reference with a coverageData >= 13X There is a 3.13% of reference with a coverageData >= 14X There is a 1.96% of reference with a coverageData >= 15X There is a 1.25% of reference with a coverageData >= 16X There is a 0.83% of reference with a coverageData >= 17X There is a 0.58% of reference with a coverageData >= 18X There is a 0.43% of reference with a coverageData >= 19X There is a 0.35% of reference with a coverageData >= 20X There is a 0.29% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.19% of reference with a coverageData >= 25X There is a 0.18% of reference with a coverageData >= 26X There is a 0.17% of reference with a coverageData >= 27X There is a 0.16% of reference with a coverageData >= 28X There is a 0.15% of reference with a coverageData >= 29X There is a 0.14% of reference with a coverageData >= 30X There is a 0.14% of reference with a coverageData >= 31X There is a 0.13% of reference with a coverageData >= 32X There is a 0.12% of reference with a coverageData >= 33X There is a 0.12% of reference with a coverageData >= 34X There is a 0.11% of reference with a coverageData >= 35X There is a 0.11% of reference with a coverageData >= 36X There is a 0.1% of reference with a coverageData >= 37X There is a 0.1% of reference with a coverageData >= 38X There is a 0.1% of reference with a coverageData >= 39X There is a 0.09% of reference with a coverageData >= 40X There is a 0.09% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.08% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.07% of reference with a coverageData >= 46X There is a 0.07% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.07% of reference with a coverageData >= 50X There is a 0.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1684914951 6.759922780693895 148.4860302462331 chr2 243199373 1786477599 7.345732749894878 39.174120933898564 chr3 198022430 1390322867 7.021037298653491 4.535906470599097 chr4 191154276 1406242894 7.356586122091247 44.617202123332675 chr5 180915260 1268550056 7.0118466291898205 6.082133041858494 chr6 171115067 1214047376 7.094918041320113 34.044935571250505 chr7 159138663 1128236706 7.089645499912237 44.35803354739148 chr8 146364022 1066499029 7.286620129911434 99.17201357006593 chr9 141213431 875487293 6.1997452140370415 65.2278846061794 chr10 135534747 1065746077 7.863268280568672 115.53582821571268 chr11 135006516 949485727 7.032888153339206 29.85782198974632 chr12 133851895 922802815 6.8942080722876575 5.543206585595506 chr13 115169878 675877047 5.868522731264854 4.2073067309370895 chr14 107349540 627034946 5.841058527125501 5.91017645118598 chr15 102531392 595403962 5.807040657362771 4.657299012984933 chr16 90354753 627544615 6.945341491885878 43.53291355348582 chr17 81195210 559272046 6.887993097129744 36.05226231923069 chr18 78077248 583360256 7.471578096605044 84.55899615864293 chr19 59128983 394478119 6.671484929818597 67.82097282878348 chr20 63025520 425916592 6.757843362498239 13.539556743987246 chr21 48129895 289676754 6.018645043792429 26.561860047846157 chr22 51304566 250363848 4.879952556269553 33.000249613639774 chrMT 16571 5971743 360.3731217186651 46.68891642460527 chrX 155270560 564288266 3.6342257411836476 12.659475052636264 chrY 59373566 244284015 4.114356462941775 69.04380015207846