BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6432729.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP127755/SRP127755.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 = 379,687,448 number of mapped reads = 379,515,021 (99.95%) number of supplementary alignments = 223,752 (0.06%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 189,764,891 number of mapped paired reads (second in pair) = 189,750,130 number of mapped paired reads (both in pair) = 379,449,242 number of mapped paired reads (singletons) = 65,779 number of mapped bases = 52,050,727,066 bp number of sequenced bases = 51,999,866,604 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 176,164,448 duplication rate = 31.19% >>>>>>> Insert size mean insert size = 86,777.6566 std insert size = 2,990,056.0962 median insert size = 305 >>>>>>> Mapping quality mean mapping quality = 55.3561 >>>>>>> ACTG content number of A's = 14,221,941,159 bp (27.35%) number of C's = 11,290,691,129 bp (21.71%) number of T's = 14,028,585,886 bp (26.98%) number of G's = 12,456,995,447 bp (23.96%) number of N's = 1,652,983 bp (0%) GC percentage = 45.67% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 543,425,503 number of insertions = 10,871,113 mapped reads with insertion percentage = 2.8% number of deletions = 34,215,265 mapped reads with deletion percentage = 8.6% homopolymer indels = 51.28% >>>>>>> Coverage mean coverageData = 16.8139X std coverageData = 49.1567X There is a 65.53% of reference with a coverageData >= 1X There is a 56.23% of reference with a coverageData >= 2X There is a 49.84% of reference with a coverageData >= 3X There is a 45.04% of reference with a coverageData >= 4X There is a 41.21% of reference with a coverageData >= 5X There is a 38.05% of reference with a coverageData >= 6X There is a 35.39% of reference with a coverageData >= 7X There is a 33.1% of reference with a coverageData >= 8X There is a 31.11% of reference with a coverageData >= 9X There is a 29.36% of reference with a coverageData >= 10X There is a 27.79% of reference with a coverageData >= 11X There is a 26.39% of reference with a coverageData >= 12X There is a 25.12% of reference with a coverageData >= 13X There is a 23.97% of reference with a coverageData >= 14X There is a 22.91% of reference with a coverageData >= 15X There is a 21.94% of reference with a coverageData >= 16X There is a 21.05% of reference with a coverageData >= 17X There is a 20.23% of reference with a coverageData >= 18X There is a 19.46% of reference with a coverageData >= 19X There is a 18.74% of reference with a coverageData >= 20X There is a 18.08% of reference with a coverageData >= 21X There is a 17.45% of reference with a coverageData >= 22X There is a 16.87% of reference with a coverageData >= 23X There is a 16.31% of reference with a coverageData >= 24X There is a 15.79% of reference with a coverageData >= 25X There is a 15.3% of reference with a coverageData >= 26X There is a 14.84% of reference with a coverageData >= 27X There is a 14.4% of reference with a coverageData >= 28X There is a 13.98% of reference with a coverageData >= 29X There is a 13.59% of reference with a coverageData >= 30X There is a 13.21% of reference with a coverageData >= 31X There is a 12.85% of reference with a coverageData >= 32X There is a 12.51% of reference with a coverageData >= 33X There is a 12.18% of reference with a coverageData >= 34X There is a 11.87% of reference with a coverageData >= 35X There is a 11.57% of reference with a coverageData >= 36X There is a 11.28% of reference with a coverageData >= 37X There is a 11% of reference with a coverageData >= 38X There is a 10.74% of reference with a coverageData >= 39X There is a 10.49% of reference with a coverageData >= 40X There is a 10.24% of reference with a coverageData >= 41X There is a 10.01% of reference with a coverageData >= 42X There is a 9.78% of reference with a coverageData >= 43X There is a 9.56% of reference with a coverageData >= 44X There is a 9.35% of reference with a coverageData >= 45X There is a 9.15% of reference with a coverageData >= 46X There is a 8.96% of reference with a coverageData >= 47X There is a 8.77% of reference with a coverageData >= 48X There is a 8.58% of reference with a coverageData >= 49X There is a 8.41% of reference with a coverageData >= 50X There is a 8.24% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4836791724 19.405334697240335 55.269859994173196 chr2 243199373 4440838989 18.260075814422432 55.95802770001604 chr3 198022430 3313929548 16.735122117226823 44.56155775629679 chr4 191154276 2371313418 12.405233446098794 36.810329391992774 chr5 180915260 2930627880 16.198898202395974 45.55056516938164 chr6 171115067 3001839250 17.542810826822166 48.315019016425566 chr7 159138663 2641947413 16.601543353421288 45.73274379324534 chr8 146364022 2484060266 16.971795609716164 46.24804263878714 chr9 141213431 2227808492 15.77617990175453 51.05615144919902 chr10 135534747 2660032595 19.626204009514993 52.10267372332819 chr11 135006516 2778353195 20.579400737961418 53.90267954940148 chr12 133851895 2316606480 17.30723707721882 47.804492363605696 chr13 115169878 1294156652 11.236936901157437 35.18879472361468 chr14 107349540 1617976068 15.07203540881498 44.492670671585124 chr15 102531392 1742714899 16.996891049718705 49.35862397443158 chr16 90354753 1876605010 20.76930042628748 63.17225952424445 chr17 81195210 1973445847 24.304954036081686 62.42974156893101 chr18 78077248 1200945090 15.381498717782677 44.98762014035419 chr19 59128983 1501148650 25.387696081294006 68.61712077780226 chr20 63025520 1595443664 25.314248323536244 61.86978488447031 chr21 48129895 672051465 13.963285500622845 51.11286534558333 chr22 51304566 1008523323 19.6575743960099 58.28717451343413 chrMT 16571 4978175 300.41488141934707 593.0452644873599 chrX 155270560 1391868970 8.964152444610233 26.048608016683133 chrY 59373566 166720003 2.8079836572389807 21.73897108936544