BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695988.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 17,769,833 number of mapped reads = 16,340,435 (91.96%) number of supplementary alignments = 271,208 (1.53%) number of secondary alignments = 0 number of mapped bases = 2,452,250,179 bp number of sequenced bases = 2,435,721,160 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,841,551 duplication rate = 20.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.2709 >>>>>>> ACTG content number of A's = 698,782,509 bp (28.69%) number of C's = 516,125,577 bp (21.19%) number of T's = 694,137,758 bp (28.5%) number of G's = 526,675,316 bp (21.62%) number of N's = 0 bp (0%) GC percentage = 42.81% >>>>>>> Mismatches and indels general error rate = 0.0163 number of mismatches = 25,279,896 number of insertions = 13,314,267 mapped reads with insertion percentage = 46.19% number of deletions = 14,836,334 mapped reads with deletion percentage = 51.88% homopolymer indels = 37.78% >>>>>>> Coverage mean coverageData = 0.7921X std coverageData = 2.0371X There is a 28.99% of reference with a coverageData >= 1X There is a 16.69% of reference with a coverageData >= 2X There is a 10.22% of reference with a coverageData >= 3X There is a 6.56% of reference with a coverageData >= 4X There is a 4.38% of reference with a coverageData >= 5X There is a 3.01% of reference with a coverageData >= 6X There is a 2.12% of reference with a coverageData >= 7X There is a 1.52% of reference with a coverageData >= 8X There is a 1.12% of reference with a coverageData >= 9X There is a 0.83% of reference with a coverageData >= 10X There is a 0.63% of reference with a coverageData >= 11X There is a 0.48% of reference with a coverageData >= 12X There is a 0.37% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.23% of reference with a coverageData >= 15X There is a 0.18% of reference with a coverageData >= 16X There is a 0.15% of reference with a coverageData >= 17X There is a 0.12% of reference with a coverageData >= 18X There is a 0.1% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% 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 227750895 0.9137425378771674 2.644131351565994 chr2 243199373 207870068 0.8547311016299372 2.0619193438219887 chr3 198022430 169564336 0.8562885325667401 1.942115392680508 chr4 191154276 138935257 0.7268226476921709 1.788850014656741 chr5 180915260 151699588 0.8385118425057123 1.9539253752586672 chr6 171115067 141372220 0.826182185347828 1.9975503142133917 chr7 159138663 130994409 0.8231463462778998 1.9144510115624984 chr8 146364022 129972163 0.888006227377381 2.0093975889429223 chr9 141213431 102985584 0.7292902896750664 1.955702568135564 chr10 135534747 117997662 0.8706081990915584 2.2402530212778666 chr11 135006516 112122165 0.8304944703557864 2.071250720137955 chr12 133851895 122527136 0.9153933606991519 2.0260377281384723 chr13 115169878 64562772 0.5605873091226162 1.5060847018198313 chr14 107349540 76730297 0.7147706175545792 1.8778332346970745 chr15 102531392 78164716 0.7623491154787014 1.8518909104699248 chr16 90354753 86285926 0.954968312513676 2.2490717278774173 chr17 81195210 71429795 0.8797291736790878 2.5091183471589056 chr18 78077248 60774515 0.7783895636280623 2.3043535480544333 chr19 59128983 55708334 0.9421493686099759 2.4593301261062486 chr20 63025520 58319152 0.9253259949303076 2.151474648113041 chr21 48129895 30399648 0.6316167529557253 1.8573638380947937 chr22 51304566 33160825 0.646352314918715 1.7612977588330012 chrMT 16571 409800 24.729949912497737 14.466555874907373 chrX 155270560 72249119 0.46531112530282626 1.3946868150594516 chrY 59373566 10263797 0.17286812451184083 1.2030522617542263