BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085091.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 = 1,878,368 number of mapped reads = 1,533,027 (81.61%) number of supplementary alignments = 8,012 (0.43%) number of secondary alignments = 0 number of mapped bases = 92,489,083 bp number of sequenced bases = 92,459,056 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,183 duplication rate = 1.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.4594 >>>>>>> ACTG content number of A's = 26,853,470 bp (29.04%) number of C's = 18,462,360 bp (19.97%) number of T's = 26,145,935 bp (28.28%) number of G's = 20,995,288 bp (22.71%) number of N's = 2,003 bp (0%) GC percentage = 42.68% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 825,667 number of insertions = 7,375 mapped reads with insertion percentage = 0.48% number of deletions = 18,682 mapped reads with deletion percentage = 1.21% homopolymer indels = 43.65% >>>>>>> Coverage mean coverageData = 0.0299X std coverageData = 0.2548X There is a 2.72% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 8014093 0.0321527503837192 0.39126565364836025 chr2 243199373 8816578 0.03625247010813634 0.2958230600640411 chr3 198022430 5858558 0.029585325258355832 0.18677846562813163 chr4 191154276 5302654 0.027740179874396323 0.18740071304816142 chr5 180915260 4083902 0.022573562893478415 0.16112088616956108 chr6 171115067 6388672 0.03733553165134196 0.2476961424861961 chr7 159138663 9143181 0.057454177555833805 0.3024110867716854 chr8 146364022 5457508 0.03728722349540244 0.35541351728630355 chr9 141213431 2764932 0.0195798089489094 0.22238031410354522 chr10 135534747 6557942 0.048385688136489455 0.3683341321506395 chr11 135006516 4049638 0.029995870717825206 0.2550028984300826 chr12 133851895 3471939 0.025938661533331298 0.17554411346225265 chr13 115169878 1974737 0.017146297576176993 0.13823688284771962 chr14 107349540 2869528 0.02673069675007457 0.18361169918186973 chr15 102531392 1777410 0.0173352762049695 0.14025026477828617 chr16 90354753 2726249 0.03017272373042733 0.20134478168066483 chr17 81195210 1532226 0.018870891521802824 0.1656537314102681 chr18 78077248 2219533 0.028427397953370487 0.3778978365836433 chr19 59128983 1371273 0.023191215719032408 0.29866760222179534 chr20 63025520 1994750 0.03164987770033472 0.1935534249930194 chr21 48129895 1085568 0.022554962980908227 0.1725740155614451 chr22 51304566 678017 0.013215529393621613 0.12243023400033785 chrMT 16571 6925 0.41789873876048517 0.6794803090429372 chrX 155270560 4118341 0.026523643632121893 0.19479742853266382 chrY 59373566 224929 0.0037883693898392427 0.09457875997616111