BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081235.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 = 1,873,736 number of mapped reads = 1,664,341 (88.82%) number of supplementary alignments = 22,136 (1.18%) number of secondary alignments = 0 number of mapped bases = 110,208,510 bp number of sequenced bases = 110,166,450 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,122 duplication rate = 3.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6595 >>>>>>> ACTG content number of A's = 31,386,242 bp (28.49%) number of C's = 21,052,020 bp (19.11%) number of T's = 33,929,556 bp (30.8%) number of G's = 23,793,927 bp (21.6%) number of N's = 4,705 bp (0%) GC percentage = 40.71% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 921,172 number of insertions = 8,281 mapped reads with insertion percentage = 0.49% number of deletions = 25,435 mapped reads with deletion percentage = 1.51% homopolymer indels = 48.41% >>>>>>> Coverage mean coverageData = 0.0356X std coverageData = 0.2708X There is a 2.96% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 11080659 0.04445589325131511 0.4222492454063556 chr2 243199373 6318950 0.02598259165742175 0.28467395749355634 chr3 198022430 6954643 0.03512048104853577 0.21929245899810276 chr4 191154276 4252556 0.022246721804957164 0.1789587971235515 chr5 180915260 7740432 0.04278484855285287 0.24101571893550877 chr6 171115067 7583163 0.04431616182577306 0.2602527893341012 chr7 159138663 7085421 0.04452356747524013 0.33261008920431684 chr8 146364022 7027024 0.04801059648388181 0.3164468294382344 chr9 141213431 2994419 0.02120491640770346 0.20110225520849928 chr10 135534747 3510080 0.025898008279751316 0.2568792609962726 chr11 135006516 6311788 0.04675172863508306 0.3303722000160235 chr12 133851895 2784630 0.020803814544426136 0.1686516231028649 chr13 115169878 3104427 0.026955199171088816 0.19157842631738917 chr14 107349540 4248186 0.039573397333607575 0.2346912468708963 chr15 102531392 3702592 0.03611178906066154 0.2254570009531564 chr16 90354753 3686229 0.04079728932466895 0.23970987100343583 chr17 81195210 1509550 0.018591613963434544 0.17575781837902435 chr18 78077248 3692633 0.047294610076420725 0.32779282134899485 chr19 59128983 3135617 0.05303011891816235 0.3635667939570634 chr20 63025520 2383389 0.03781625284487934 0.22774598430599424 chr21 48129895 1351693 0.028084270701193095 0.19959959868074587 chr22 51304566 694332 0.013533532278589005 0.1329097661011078 chrMT 16571 18963 1.1443485607386399 1.3935963585686224 chrX 155270560 8738844 0.05628139680825522 0.29229031329789457 chrY 59373566 298290 0.005023952915342831 0.09814512387062474