BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549003.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,184,418 number of mapped reads = 8,811,138 (86.52%) number of secondary alignments = 0 number of mapped bases = 349,922,397 bp number of sequenced bases = 349,883,685 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 798,764 duplication rate = 8.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5072 >>>>>>> ACTG content number of A's = 104,926,320 bp (29.99%) number of C's = 69,330,687 bp (19.82%) number of T's = 105,366,508 bp (30.11%) number of G's = 70,256,582 bp (20.08%) number of N's = 3,588 bp (0%) GC percentage = 39.9% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 998,579 number of insertions = 10,484 mapped reads with insertion percentage = 0.12% number of deletions = 29,738 mapped reads with deletion percentage = 0.34% homopolymer indels = 43.93% >>>>>>> Coverage mean coverageData = 0.113X std coverageData = 0.9536X There is a 8.28% of reference with a coverageData >= 1X There is a 2.08% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 28704174 0.11516189562472544 1.4597214435822918 chr2 243199373 30783926 0.12657896942851082 0.6078344569429671 chr3 198022430 23688911 0.1196274129147895 0.4440416630860452 chr4 191154276 25118754 0.13140566104835658 0.5070341135732692 chr5 180915260 23692733 0.13096038996378748 0.4680012676129966 chr6 171115067 22614612 0.13216026149234422 0.5542473143996205 chr7 159138663 19035978 0.11961881318558018 0.9540110901661878 chr8 146364022 18332453 0.125252454459061 3.022077710208483 chr9 141213431 15307339 0.10839860551224763 0.5494616998132849 chr10 135534747 17391338 0.12831645304948996 0.6867905255455977 chr11 135006516 15861567 0.11748741816283889 0.574985341796587 chr12 133851895 14957992 0.11175031926144938 0.4481337939700373 chr13 115169878 12341448 0.10715864438095524 0.4156085304312514 chr14 107349540 11145066 0.10382034240668381 0.4989867171732595 chr15 102531392 9092716 0.08868226425717501 0.37724281444971525 chr16 90354753 9220538 0.10204817891539142 0.4556040949731346 chr17 81195210 7791922 0.09596529154860244 0.4309856360595045 chr18 78077248 8789768 0.11257784085832534 1.1836963174211375 chr19 59128983 5365150 0.09073638219010126 1.0752639323143538 chr20 63025520 7287905 0.11563419072147282 0.45971083815595243 chr21 48129895 4580604 0.09517170149654389 0.47173630091913094 chr22 51304566 3356738 0.0654276658338753 0.3554047666685566 chrMT 16571 2698 0.1628145555488504 0.44846181225476023 chrX 155270560 12318557 0.07933607633024574 0.45536722577202593 chrY 59373566 3139510 0.05287723496345158 0.5449852980186255