BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084390.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,551,668 number of mapped reads = 2,321,930 (91%) number of supplementary alignments = 13,215 (0.52%) number of secondary alignments = 0 number of mapped bases = 155,286,636 bp number of sequenced bases = 155,229,687 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,757 duplication rate = 2.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.401 >>>>>>> ACTG content number of A's = 43,532,131 bp (28.04%) number of C's = 29,859,142 bp (19.24%) number of T's = 47,892,586 bp (30.85%) number of G's = 33,746,994 bp (21.74%) number of N's = 198,834 bp (0.13%) GC percentage = 40.98% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 1,582,001 number of insertions = 10,930 mapped reads with insertion percentage = 0.47% number of deletions = 32,133 mapped reads with deletion percentage = 1.37% homopolymer indels = 47.99% >>>>>>> Coverage mean coverageData = 0.0502X std coverageData = 0.3057X There is a 4.21% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 15092668 0.060552178122757816 0.42935917719165223 chr2 243199373 15146295 0.06227933408364503 0.34272901972335 chr3 198022430 10604240 0.05355070130186767 0.2663577037340838 chr4 191154276 7158119 0.037446815994845964 0.22733504589619669 chr5 180915260 8063966 0.04457316646478578 0.2417381122534102 chr6 171115067 7439128 0.04347441829888656 0.26160552200926435 chr7 159138663 8767133 0.05509115657205189 0.4105147585902901 chr8 146364022 7668531 0.05239355201649214 0.3163964686248113 chr9 141213431 5472914 0.03875632764704938 0.2560194832716622 chr10 135534747 11211651 0.08272159905975993 0.40697292345176717 chr11 135006516 8666027 0.064189694370011 0.34288177821115406 chr12 133851895 8001996 0.05978246329646659 0.28242606014444754 chr13 115169878 3798563 0.03298226121243265 0.20970809651022101 chr14 107349540 4126266 0.038437668200534444 0.23015500948174905 chr15 102531392 3634035 0.035443145061368135 0.22227706651054344 chr16 90354753 3364446 0.03723596034842794 0.23438993799008498 chr17 81195210 4250347 0.05234726284961884 0.27667032224602467 chr18 78077248 4141923 0.05304903933089445 0.38689809231025074 chr19 59128983 3127950 0.05290045323458379 0.33571132753418315 chr20 63025520 3024653 0.0479909249459584 0.25295637603495125 chr21 48129895 1512944 0.03143460005470612 0.21031641282283253 chr22 51304566 1269169 0.024737934631393236 0.1778973351347036 chrMT 16571 68987 4.163116287490194 3.214510219656941 chrX 155270560 9384672 0.060440768681455134 0.3024712776384605 chrY 59373566 290013 0.004884547443217408 0.09556280195604448