BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365378.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 927,732,918 number of mapped reads = 893,588,339 (96.32%) number of supplementary alignments = 7,864,252 (0.85%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 445,393,449 number of mapped paired reads (second in pair) = 448,194,890 number of mapped paired reads (both in pair) = 889,349,910 number of mapped paired reads (singletons) = 4,238,429 number of mapped bases = 107,999,934,759 bp number of sequenced bases = 107,963,822,560 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 213,721,048 duplication rate = 19.44% >>>>>>> Insert size mean insert size = 96,235.6413 std insert size = 3,022,623.6867 median insert size = 204 >>>>>>> Mapping quality mean mapping quality = 54.019 >>>>>>> ACTG content number of A's = 31,967,444,205 bp (29.61%) number of C's = 22,048,744,904 bp (20.42%) number of T's = 31,602,431,331 bp (29.27%) number of G's = 22,325,450,646 bp (20.68%) number of N's = 19,751,474 bp (0.02%) GC percentage = 41.1% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 567,126,893 number of insertions = 11,062,521 mapped reads with insertion percentage = 1.17% number of deletions = 13,550,487 mapped reads with deletion percentage = 1.45% homopolymer indels = 40.75% >>>>>>> Coverage mean coverageData = 34.8871X std coverageData = 453.6793X There is a 92.34% of reference with a coverageData >= 1X There is a 92.31% of reference with a coverageData >= 2X There is a 92.28% of reference with a coverageData >= 3X There is a 92.24% of reference with a coverageData >= 4X There is a 92.2% of reference with a coverageData >= 5X There is a 92.14% of reference with a coverageData >= 6X There is a 92.06% of reference with a coverageData >= 7X There is a 91.96% of reference with a coverageData >= 8X There is a 91.82% of reference with a coverageData >= 9X There is a 91.63% of reference with a coverageData >= 10X There is a 91.39% of reference with a coverageData >= 11X There is a 91.09% of reference with a coverageData >= 12X There is a 90.72% of reference with a coverageData >= 13X There is a 90.27% of reference with a coverageData >= 14X There is a 89.75% of reference with a coverageData >= 15X There is a 89.16% of reference with a coverageData >= 16X There is a 88.5% of reference with a coverageData >= 17X There is a 87.78% of reference with a coverageData >= 18X There is a 86.99% of reference with a coverageData >= 19X There is a 86.15% of reference with a coverageData >= 20X There is a 85.24% of reference with a coverageData >= 21X There is a 84.24% of reference with a coverageData >= 22X There is a 83.15% of reference with a coverageData >= 23X There is a 81.93% of reference with a coverageData >= 24X There is a 80.54% of reference with a coverageData >= 25X There is a 78.95% of reference with a coverageData >= 26X There is a 77.13% of reference with a coverageData >= 27X There is a 75.05% of reference with a coverageData >= 28X There is a 72.68% of reference with a coverageData >= 29X There is a 70% of reference with a coverageData >= 30X There is a 67.02% of reference with a coverageData >= 31X There is a 63.74% of reference with a coverageData >= 32X There is a 60.18% of reference with a coverageData >= 33X There is a 56.39% of reference with a coverageData >= 34X There is a 52.41% of reference with a coverageData >= 35X There is a 48.3% of reference with a coverageData >= 36X There is a 44.12% of reference with a coverageData >= 37X There is a 39.94% of reference with a coverageData >= 38X There is a 35.83% of reference with a coverageData >= 39X There is a 31.84% of reference with a coverageData >= 40X There is a 28.04% of reference with a coverageData >= 41X There is a 24.46% of reference with a coverageData >= 42X There is a 21.15% of reference with a coverageData >= 43X There is a 18.12% of reference with a coverageData >= 44X There is a 15.4% of reference with a coverageData >= 45X There is a 12.98% of reference with a coverageData >= 46X There is a 10.85% of reference with a coverageData >= 47X There is a 9.02% of reference with a coverageData >= 48X There is a 7.45% of reference with a coverageData >= 49X There is a 6.12% of reference with a coverageData >= 50X There is a 5.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8979037055 36.024131129446616 1187.0970423871581 chr2 243199373 9335845550 38.38762178881111 247.72874021706542 chr3 198022430 7206551485 36.39260201483236 50.39804469688698 chr4 191154276 7312052348 38.25209930433363 314.45937790646263 chr5 180915260 6583531135 36.390137211200425 30.228046774727066 chr6 171115067 6271973476 36.65354305708217 141.84302933011836 chr7 159138663 5916416634 37.177745008452156 293.113710625033 chr8 146364022 5528953546 37.77535948007769 373.9115925394436 chr9 141213431 4612636167 32.66428791040422 416.13344381938157 chr10 135534747 5858333517 43.22384957858814 949.2219630141892 chr11 135006516 5007652867 37.09193463669561 246.31138229902308 chr12 133851895 4816464494 35.98353608665757 54.19419242581539 chr13 115169878 3483782548 30.249077349895256 17.57277619430587 chr14 107349540 3283288312 30.58502450965323 28.47452833606308 chr15 102531392 3003705074 29.29546761639596 27.9635247260557 chr16 90354753 3202944424 35.44854385247448 136.05742613603977 chr17 81195210 2999715465 36.944488043075445 203.33425915790625 chr18 78077248 3039070523 38.923893974849115 454.33841891803024 chr19 59128983 2149269656 36.34883515584904 524.4498805127616 chr20 63025520 2260677447 35.869239111394876 90.51171338521809 chr21 48129895 1531591001 31.822030798114145 155.23637023436115 chr22 51304566 1341044491 26.138891633933714 106.62808592173214 chrMT 16571 197461501 11916.088407458814 876.3674235661362 chrX 155270560 2925376307 18.840508509790908 95.11070279532998 chrY 59373566 1152559736 19.412001226269616 502.297243506287