BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438261.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 = 758,121,248 number of mapped reads = 755,837,574 (99.7%) number of supplementary alignments = 14,591,773 (1.92%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 378,151,399 number of mapped paired reads (second in pair) = 377,686,175 number of mapped paired reads (both in pair) = 754,511,470 number of mapped paired reads (singletons) = 1,326,104 number of mapped bases = 91,609,207,523 bp number of sequenced bases = 91,589,610,124 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 270,851,417 duplication rate = 34.83% >>>>>>> Insert size mean insert size = 158,913.4258 std insert size = 3,928,626.7821 median insert size = 168 >>>>>>> Mapping quality mean mapping quality = 53.5676 >>>>>>> ACTG content number of A's = 28,112,766,094 bp (30.69%) number of C's = 17,889,493,766 bp (19.53%) number of T's = 27,496,074,245 bp (30.02%) number of G's = 18,091,062,540 bp (19.75%) number of N's = 213,479 bp (0%) GC percentage = 39.28% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 243,379,986 number of insertions = 13,197,834 mapped reads with insertion percentage = 1.73% number of deletions = 8,697,778 mapped reads with deletion percentage = 1.14% homopolymer indels = 49.59% >>>>>>> Coverage mean coverageData = 29.5925X std coverageData = 188.538X There is a 87.3% of reference with a coverageData >= 1X There is a 85.15% of reference with a coverageData >= 2X There is a 82.39% of reference with a coverageData >= 3X There is a 80.01% of reference with a coverageData >= 4X There is a 77.53% of reference with a coverageData >= 5X There is a 75.16% of reference with a coverageData >= 6X There is a 72.81% of reference with a coverageData >= 7X There is a 70.52% of reference with a coverageData >= 8X There is a 68.26% of reference with a coverageData >= 9X There is a 66.07% of reference with a coverageData >= 10X There is a 63.93% of reference with a coverageData >= 11X There is a 61.84% of reference with a coverageData >= 12X There is a 59.81% of reference with a coverageData >= 13X There is a 57.84% of reference with a coverageData >= 14X There is a 55.92% of reference with a coverageData >= 15X There is a 54.07% of reference with a coverageData >= 16X There is a 52.27% of reference with a coverageData >= 17X There is a 50.53% of reference with a coverageData >= 18X There is a 48.85% of reference with a coverageData >= 19X There is a 47.22% of reference with a coverageData >= 20X There is a 45.65% of reference with a coverageData >= 21X There is a 44.14% of reference with a coverageData >= 22X There is a 42.68% of reference with a coverageData >= 23X There is a 41.27% of reference with a coverageData >= 24X There is a 39.91% of reference with a coverageData >= 25X There is a 38.6% of reference with a coverageData >= 26X There is a 37.34% of reference with a coverageData >= 27X There is a 36.13% of reference with a coverageData >= 28X There is a 34.96% of reference with a coverageData >= 29X There is a 33.83% of reference with a coverageData >= 30X There is a 32.74% of reference with a coverageData >= 31X There is a 31.69% of reference with a coverageData >= 32X There is a 30.68% of reference with a coverageData >= 33X There is a 29.71% of reference with a coverageData >= 34X There is a 28.77% of reference with a coverageData >= 35X There is a 27.86% of reference with a coverageData >= 36X There is a 26.99% of reference with a coverageData >= 37X There is a 26.16% of reference with a coverageData >= 38X There is a 25.35% of reference with a coverageData >= 39X There is a 24.57% of reference with a coverageData >= 40X There is a 23.82% of reference with a coverageData >= 41X There is a 23.1% of reference with a coverageData >= 42X There is a 22.4% of reference with a coverageData >= 43X There is a 21.73% of reference with a coverageData >= 44X There is a 21.08% of reference with a coverageData >= 45X There is a 20.45% of reference with a coverageData >= 46X There is a 19.85% of reference with a coverageData >= 47X There is a 19.27% of reference with a coverageData >= 48X There is a 18.71% of reference with a coverageData >= 49X There is a 18.17% of reference with a coverageData >= 50X There is a 17.65% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7154911991 28.70569374027758 38.97150784439836 chr2 243199373 7897742720 32.47435477557748 659.7600101747902 chr3 198022430 6811235531 34.396282941280944 39.04336197384527 chr4 191154276 7013360644 36.68953052350239 39.41887252205823 chr5 180915260 6106880526 33.75547494445742 38.0608941188864 chr6 171115067 5901877973 34.490697262795685 39.687115955131794 chr7 159138663 5027427804 31.5914920310723 37.95988318261703 chr8 146364022 4885758292 33.38086932320021 38.46051662440713 chr9 141213431 3760589471 26.63053680070984 36.95852768680672 chr10 135534747 3817799780 28.16842075191242 34.50857063562259 chr11 135006516 4219738146 31.255810986189733 38.588824031895776 chr12 133851895 4298626938 32.1148007504862 39.57837786515195 chr13 115169878 3173857602 27.558053000629208 35.092840697397115 chr14 107349540 2929994209 27.293961473891738 37.43981465639542 chr15 102531392 2465027856 24.041689163841646 37.57921246572609 chr16 90354753 1705825933 18.87920531419083 28.86828895975305 chr17 81195210 1415811498 17.437130811041687 26.556191491553403 chr18 78077248 2351000290 30.11120845345369 34.688656795305334 chr19 59128983 713924429 12.074018404815114 20.082248918363053 chr20 63025520 1361544162 21.60306114094735 32.49764012512002 chr21 48129895 939342253 19.516814923448305 31.191858635727595 chr22 51304566 430891212 8.398691297768702 17.52214802700967 chrMT 16571 198971 12.007181220203972 6.203386707835063 chrX 155270560 7171353014 46.18617343815853 53.5041552780587 chrY 59373566 54486278 0.9176857930345635 6.326952389002985