BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082320.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 = 2,650,089 number of mapped reads = 2,359,821 (89.05%) number of supplementary alignments = 17,921 (0.68%) number of secondary alignments = 0 number of mapped bases = 157,802,202 bp number of sequenced bases = 157,747,225 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,888 duplication rate = 3.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7619 >>>>>>> ACTG content number of A's = 43,771,948 bp (27.75%) number of C's = 29,130,857 bp (18.47%) number of T's = 49,494,513 bp (31.38%) number of G's = 35,346,563 bp (22.41%) number of N's = 3,344 bp (0%) GC percentage = 40.87% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,307,601 number of insertions = 12,509 mapped reads with insertion percentage = 0.53% number of deletions = 34,356 mapped reads with deletion percentage = 1.44% homopolymer indels = 47.52% >>>>>>> Coverage mean coverageData = 0.051X std coverageData = 0.4316X There is a 4.41% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.07% 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 0.01% 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 12385654 0.04969156726795076 0.7358970771790482 chr2 243199373 13553964 0.055731903552234896 0.5829220588639136 chr3 198022430 10724909 0.0541600716646089 0.26040005588971304 chr4 191154276 10690208 0.0559245036192651 0.27590817949654206 chr5 180915260 9814317 0.05424814357838029 0.26323375456391374 chr6 171115067 9316855 0.05444789382573774 0.32475796973140897 chr7 159138663 8839445 0.0555455527485486 0.5423823065325748 chr8 146364022 8223860 0.056187715311622144 0.6974874360312533 chr9 141213431 6622821 0.04689937035805043 0.3997327125602331 chr10 135534747 7335518 0.05412278520725021 0.3763278006682316 chr11 135006516 7112767 0.05268462005196845 0.359357145523093 chr12 133851895 7216798 0.053916293079003474 0.2655601493781017 chr13 115169878 5216875 0.0452972173852611 0.2377115936132635 chr14 107349540 4810027 0.04480715054764091 0.2547530261220289 chr15 102531392 4378611 0.0427050770948277 0.2370416579103436 chr16 90354753 4256053 0.04710380869504452 0.27451215691420316 chr17 81195210 3855897 0.04748921765212505 0.27018917650975177 chr18 78077248 4288492 0.054926269942301244 0.7080940574347622 chr19 59128983 2858040 0.0483356867477325 0.5454108484636427 chr20 63025520 3020704 0.047928267787397866 0.25292658971738924 chr21 48129895 2078879 0.04319309235974855 0.25134993259441213 chr22 51304566 1553844 0.03028666103519909 0.193440602415882 chrMT 16571 4180 0.25224790296300764 0.5257019563939319 chrX 155270560 9259778 0.05963640499525474 0.3086714874027558 chrY 59373566 383706 0.006462572923445427 0.13245913052139915