BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082458.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 = 1,931,322 number of mapped reads = 1,777,020 (92.01%) number of supplementary alignments = 14,795 (0.77%) number of secondary alignments = 0 number of mapped bases = 124,443,844 bp number of sequenced bases = 124,398,202 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,783 duplication rate = 2.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5393 >>>>>>> ACTG content number of A's = 36,973,829 bp (29.72%) number of C's = 23,304,805 bp (18.73%) number of T's = 38,093,778 bp (30.62%) number of G's = 26,023,113 bp (20.92%) number of N's = 2,677 bp (0%) GC percentage = 39.65% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,039,851 number of insertions = 10,307 mapped reads with insertion percentage = 0.58% number of deletions = 27,626 mapped reads with deletion percentage = 1.54% homopolymer indels = 47.76% >>>>>>> Coverage mean coverageData = 0.0402X std coverageData = 0.3683X There is a 3.59% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.04% 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 9589393 0.038472895118684576 0.6300186124571562 chr2 243199373 10798590 0.04440221151392525 0.36284596323767193 chr3 198022430 8614739 0.04350385458859383 0.22648868398552482 chr4 191154276 8524892 0.04459692023839425 0.23471232925798616 chr5 180915260 7968454 0.04404522868883476 0.22807331144656537 chr6 171115067 7489804 0.04377056989376628 0.26812705635274037 chr7 159138663 6954536 0.0437011086363092 0.45067805165744274 chr8 146364022 6491407 0.04435111109477437 0.768553959769408 chr9 141213431 5165783 0.036581385803167686 0.314882587456542 chr10 135534747 5757039 0.04247648021949678 0.3240994393973907 chr11 135006516 5673716 0.042025497495246825 0.28375667495660195 chr12 133851895 5543417 0.041414557485346025 0.22481002723471136 chr13 115169878 4145427 0.03599402093662025 0.20371710195303783 chr14 107349540 3816180 0.035549104355733614 0.21829171544186454 chr15 102531392 3436554 0.03351709103881083 0.19837560954513178 chr16 90354753 3146113 0.03481956284026364 0.2298755041722615 chr17 81195210 2858310 0.035202938695521574 0.23163556642041713 chr18 78077248 3428638 0.04391340739878537 0.6036160981445569 chr19 59128983 2007036 0.033943353972450366 0.4624937903988702 chr20 63025520 2324375 0.03687990198256198 0.21307702419197272 chr21 48129895 1676614 0.0348351892311421 0.21544387970141446 chr22 51304566 1138097 0.022183152275374478 0.15938474106633163 chrMT 16571 2934 0.17705630318025467 0.45068631368694606 chrX 155270560 7598939 0.04893998578996559 0.2601101079099385 chrY 59373566 292857 0.004932447547448977 0.11114871790393352