BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777297.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 1,363,470 number of mapped reads = 1,291,512 (94.72%) number of supplementary alignments = 42,904 (3.15%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 647,102 number of mapped paired reads (second in pair) = 644,410 number of mapped paired reads (both in pair) = 1,285,644 number of mapped paired reads (singletons) = 5,868 number of mapped bases = 124,878,130 bp number of sequenced bases = 124,831,322 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 106,449 duplication rate = 7.18% >>>>>>> Insert size mean insert size = 126,335.8543 std insert size = 3,395,461.5405 median insert size = 158 >>>>>>> Mapping quality mean mapping quality = 53.1844 >>>>>>> ACTG content number of A's = 36,989,293 bp (29.63%) number of C's = 25,477,487 bp (20.41%) number of T's = 36,201,125 bp (29%) number of G's = 26,161,296 bp (20.96%) number of N's = 2,121 bp (0%) GC percentage = 41.37% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 763,340 number of insertions = 31,343 mapped reads with insertion percentage = 2.36% number of deletions = 17,463 mapped reads with deletion percentage = 1.3% homopolymer indels = 44.85% >>>>>>> Coverage mean coverageData = 0.0403X std coverageData = 0.5117X There is a 2.83% of reference with a coverageData >= 1X There is a 0.88% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 10149588 0.04072041208675665 0.9263314050013711 chr2 243199373 11012355 0.04528118170765185 0.44583044300981284 chr3 198022430 8453095 0.0426875632220047 0.2846605484867291 chr4 191154276 8528791 0.04461731737562596 0.4793644934047444 chr5 180915260 7677739 0.04243831614867646 0.26223994347586876 chr6 171115067 7114433 0.041576893985612616 0.2913358833425698 chr7 159138663 6653122 0.04180707487783782 0.3595364328297822 chr8 146364022 6487967 0.04432760805110972 0.35657299971521245 chr9 141213431 5246112 0.03715023396039432 0.45637550006318356 chr10 135534747 7521547 0.05549534098440454 1.287268928804647 chr11 135006516 5818688 0.04309931233245068 0.2955845079506954 chr12 133851895 5547268 0.04144332809034941 0.25725574433291304 chr13 115169878 3939521 0.03420617498613657 0.2323490592581995 chr14 107349540 3714761 0.034604349492321995 0.23855811546988528 chr15 102531392 3445978 0.03360900435254015 0.2306012261720033 chr16 90354753 3984917 0.0441030147025027 0.5710459703763238 chr17 81195210 3030069 0.037318322102991054 0.3105509605046453 chr18 78077248 3413226 0.043716013146364995 0.522958906137405 chr19 59128983 2052826 0.03471776269177503 0.52493380364293 chr20 63025520 2581875 0.04096554855874256 0.2729659305406722 chr21 48129895 1622295 0.033706597531534196 0.2895029789849487 chr22 51304566 1195852 0.02330888053901479 0.19573808273461285 chrMT 16571 508909 30.71082010741657 9.351230828461736 chrX 155270560 3568810 0.022984460157804545 0.20927789715853934 chrY 59373566 1608386 0.027089260564204617 0.5816890150330007