BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438263.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 599,171,020 number of mapped reads = 597,241,380 (99.68%) number of supplementary alignments = 9,868,261 (1.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 298,723,100 number of mapped paired reads (second in pair) = 298,518,280 number of mapped paired reads (both in pair) = 595,873,434 number of mapped paired reads (singletons) = 1,367,946 number of mapped bases = 86,052,696,005 bp number of sequenced bases = 86,028,344,360 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 251,622,998 duplication rate = 39.27% >>>>>>> Insert size mean insert size = 42,994.1517 std insert size = 2,017,345.3823 median insert size = 243 >>>>>>> Mapping quality mean mapping quality = 55.088 >>>>>>> ACTG content number of A's = 25,887,025,046 bp (30.09%) number of C's = 17,303,627,765 bp (20.11%) number of T's = 24,691,151,510 bp (28.7%) number of G's = 18,146,011,054 bp (21.09%) number of N's = 528,985 bp (0%) GC percentage = 41.21% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 437,179,059 number of insertions = 10,968,567 mapped reads with insertion percentage = 1.81% number of deletions = 9,824,761 mapped reads with deletion percentage = 1.62% homopolymer indels = 48.57% >>>>>>> Coverage mean coverageData = 27.7975X std coverageData = 97.0742X There is a 91.45% of reference with a coverageData >= 1X There is a 90.66% of reference with a coverageData >= 2X There is a 89.7% of reference with a coverageData >= 3X There is a 88.6% of reference with a coverageData >= 4X There is a 87.31% of reference with a coverageData >= 5X There is a 85.87% of reference with a coverageData >= 6X There is a 84.27% of reference with a coverageData >= 7X There is a 82.53% of reference with a coverageData >= 8X There is a 80.65% of reference with a coverageData >= 9X There is a 78.67% of reference with a coverageData >= 10X There is a 76.59% of reference with a coverageData >= 11X There is a 74.43% of reference with a coverageData >= 12X There is a 72.21% of reference with a coverageData >= 13X There is a 69.94% of reference with a coverageData >= 14X There is a 67.64% of reference with a coverageData >= 15X There is a 65.33% of reference with a coverageData >= 16X There is a 63.02% of reference with a coverageData >= 17X There is a 60.72% of reference with a coverageData >= 18X There is a 58.43% of reference with a coverageData >= 19X There is a 56.17% of reference with a coverageData >= 20X There is a 53.95% of reference with a coverageData >= 21X There is a 51.77% of reference with a coverageData >= 22X There is a 49.64% of reference with a coverageData >= 23X There is a 47.57% of reference with a coverageData >= 24X There is a 45.55% of reference with a coverageData >= 25X There is a 43.59% of reference with a coverageData >= 26X There is a 41.69% of reference with a coverageData >= 27X There is a 39.86% of reference with a coverageData >= 28X There is a 38.09% of reference with a coverageData >= 29X There is a 36.38% of reference with a coverageData >= 30X There is a 34.74% of reference with a coverageData >= 31X There is a 33.16% of reference with a coverageData >= 32X There is a 31.65% of reference with a coverageData >= 33X There is a 30.2% of reference with a coverageData >= 34X There is a 28.81% of reference with a coverageData >= 35X There is a 27.48% of reference with a coverageData >= 36X There is a 26.2% of reference with a coverageData >= 37X There is a 24.98% of reference with a coverageData >= 38X There is a 23.82% of reference with a coverageData >= 39X There is a 22.71% of reference with a coverageData >= 40X There is a 21.65% of reference with a coverageData >= 41X There is a 20.64% of reference with a coverageData >= 42X There is a 19.67% of reference with a coverageData >= 43X There is a 18.75% of reference with a coverageData >= 44X There is a 17.88% of reference with a coverageData >= 45X There is a 17.04% of reference with a coverageData >= 46X There is a 16.25% of reference with a coverageData >= 47X There is a 15.49% of reference with a coverageData >= 48X There is a 14.77% of reference with a coverageData >= 49X There is a 14.09% of reference with a coverageData >= 50X There is a 13.43% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7380990578 29.612726934790665 30.622772847178847 chr2 243199373 7450153044 30.633931955079508 113.41039809755074 chr3 198022430 6086496816 30.736401002654095 154.05866739290332 chr4 191154276 5396985006 28.2336608886531 27.177727238406767 chr5 180915260 5363941312 29.648915807323274 35.272667148641695 chr6 171115067 4982311514 29.116731807141214 24.540548101369456 chr7 159138663 4599539243 28.90271387412624 26.35782235121043 chr8 146364022 4269172571 29.16818295004219 23.288788991606182 chr9 141213431 3646134943 25.82002942057261 29.398813755797057 chr10 135534747 4070649913 30.03399499465624 37.61109369140705 chr11 135006516 4255014734 31.517106433588733 26.7279383921782 chr12 133851895 4201188031 31.38684014148623 26.39265162501979 chr13 115169878 2753885086 23.91150475995121 22.534134108047514 chr14 107349540 2782142198 25.916666228844576 28.100821471263707 chr15 102531392 2660026225 25.943529811825826 27.556158450460988 chr16 90354753 2469308221 27.329035153247556 45.641804154174956 chr17 81195210 2392107830 29.461193954668015 35.64580982668873 chr18 78077248 2224567375 28.49187736483745 23.078467345814182 chr19 59128983 1554724562 26.293781545337925 210.9892606257269 chr20 63025520 2033914589 32.27128612346237 30.040089415872394 chr21 48129895 1083240884 22.50661224172627 79.052655002089 chr22 51304566 1097773266 21.397184531294933 28.184059220361977 chrMT 16571 482750989 29132.278619274635 11302.919043227435 chrX 155270560 2424636347 15.61555743084845 27.108522045771124 chrY 59373566 391040728 6.586108168069272 22.216093220523145