BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472412.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 19,608,334 number of mapped reads = 19,480,875 (99.35%) number of supplementary alignments = 68,504 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,765,859 number of mapped paired reads (second in pair) = 9,715,016 number of mapped paired reads (both in pair) = 19,401,400 number of mapped paired reads (singletons) = 79,475 number of mapped bases = 1,910,309,287 bp number of sequenced bases = 1,910,087,949 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,572,921 duplication rate = 48.13% >>>>>>> Insert size mean insert size = 16,853.971 std insert size = 1,314,566.4751 median insert size = 205 >>>>>>> Mapping quality mean mapping quality = 55.2457 >>>>>>> ACTG content number of A's = 509,430,835 bp (26.67%) number of C's = 447,056,941 bp (23.41%) number of T's = 510,647,443 bp (26.73%) number of G's = 442,714,125 bp (23.18%) number of N's = 238,605 bp (0.01%) GC percentage = 46.58% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 9,593,884 number of insertions = 108,915 mapped reads with insertion percentage = 0.55% number of deletions = 88,303 mapped reads with deletion percentage = 0.45% homopolymer indels = 45.34% >>>>>>> Coverage mean coverageData = 0.6171X std coverageData = 20.2286X There is a 5.17% of reference with a coverageData >= 1X There is a 2.3% of reference with a coverageData >= 2X There is a 0.94% of reference with a coverageData >= 3X There is a 0.7% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.42% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.36% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.32% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.31% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.29% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.27% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.26% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.25% of reference with a coverageData >= 28X There is a 0.25% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.24% of reference with a coverageData >= 32X There is a 0.23% of reference with a coverageData >= 33X There is a 0.23% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.22% of reference with a coverageData >= 37X There is a 0.22% of reference with a coverageData >= 38X There is a 0.22% of reference with a coverageData >= 39X There is a 0.21% of reference with a coverageData >= 40X There is a 0.21% of reference with a coverageData >= 41X There is a 0.21% of reference with a coverageData >= 42X There is a 0.21% of reference with a coverageData >= 43X There is a 0.2% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.2% of reference with a coverageData >= 46X There is a 0.2% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.19% of reference with a coverageData >= 49X There is a 0.19% of reference with a coverageData >= 50X There is a 0.19% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 244844307 0.982321753172282 29.577132940321473 chr2 243199373 129889289 0.5340856244723954 19.473997113365638 chr3 198022430 149018859 0.7525352506784206 17.689859111073496 chr4 191154276 65918241 0.34484314125413545 11.374587072698903 chr5 180915260 87270984 0.482385974516467 15.470974864680848 chr6 171115067 124899247 0.7299137895320463 20.719640291948696 chr7 159138663 110216494 0.692581500449077 23.164358844089165 chr8 146364022 94741876 0.6473030373543575 19.06163208204086 chr9 141213431 121033106 0.8570934446030137 28.241979752581162 chr10 135534747 44315267 0.3269660952700196 10.12251222867353 chr11 135006516 77195997 0.5717946013805734 14.553638933809612 chr12 133851895 91196552 0.6813243249189711 18.90167005552374 chr13 115169878 44031229 0.3823154957236301 19.76906457998103 chr14 107349540 40790062 0.37997425978723337 11.107638561004045 chr15 102531392 54166544 0.528292291203849 23.816407571124554 chr16 90354753 104658120 1.158302319746256 29.820447611146115 chr17 81195210 85761032 1.0562326521478298 26.581451727443422 chr18 78077248 28829066 0.369237732354501 11.896528509282975 chr19 59128983 46412400 0.784934860117584 17.43291587646573 chr20 63025520 42307035 0.6712683211499088 17.80884031549529 chr21 48129895 14791672 0.3073281585176947 16.53460154803131 chr22 51304566 42219372 0.8229164632247352 30.397722591894972 chrMT 16571 2556 0.15424536841470038 0.4187498628169308 chrX 155270560 64121930 0.4129690135721801 17.503884407449174 chrY 59373566 1678050 0.02826257732270957 0.8176250580995588