BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085088.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 = 1,794,725 number of mapped reads = 1,461,871 (81.45%) number of supplementary alignments = 8,726 (0.49%) number of secondary alignments = 0 number of mapped bases = 91,784,572 bp number of sequenced bases = 91,751,469 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,631 duplication rate = 2.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5133 >>>>>>> ACTG content number of A's = 27,082,773 bp (29.52%) number of C's = 17,582,685 bp (19.16%) number of T's = 27,316,625 bp (29.77%) number of G's = 19,767,367 bp (21.54%) number of N's = 2,019 bp (0%) GC percentage = 40.71% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 821,830 number of insertions = 7,428 mapped reads with insertion percentage = 0.5% number of deletions = 20,500 mapped reads with deletion percentage = 1.39% homopolymer indels = 45.79% >>>>>>> Coverage mean coverageData = 0.0296X std coverageData = 0.2697X There is a 2.69% 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 7355309 0.02950969177324537 0.44818181642721505 chr2 243199373 7808353 0.032106797413494974 0.27823674391726183 chr3 198022430 6047162 0.03053776281808076 0.18851316148230482 chr4 191154276 6542559 0.034226589835740846 0.20687170212011324 chr5 180915260 5684171 0.031418969300876 0.19053403603243088 chr6 171115067 5608061 0.0327736247796344 0.23193501993388618 chr7 159138663 5297892 0.033291042541937155 0.2571594905299426 chr8 146364022 5175789 0.03536244036802979 0.4525535159511693 chr9 141213431 3952900 0.02799237984664504 0.2538714702001906 chr10 135534747 4045953 0.029851776681296346 0.2866057608938967 chr11 135006516 3538056 0.026206557319055624 0.2355684169721515 chr12 133851895 4136306 0.030902110127017626 0.19105904909341204 chr13 115169878 2849218 0.02473926385508544 0.1679294704665134 chr14 107349540 2797856 0.02606304600839463 0.18675991311490006 chr15 102531392 2616312 0.02551718014322872 0.17086909307575116 chr16 90354753 2438262 0.026985431524559643 0.1949337884112213 chr17 81195210 2115791 0.026058076578655318 0.1878266399079893 chr18 78077248 2648468 0.033921123859283565 0.46509354068423964 chr19 59128983 1604163 0.027129893304608334 0.31978335599978547 chr20 63025520 1846612 0.02929943299158817 0.19103584911136376 chr21 48129895 1236993 0.025701136476611885 0.18317494147128263 chr22 51304566 865788 0.016875457049963155 0.13861185680199747 chrMT 16571 37655 2.272343250256472 2.0175237051013184 chrX 155270560 5294812 0.03410055325362387 0.21769611233333513 chrY 59373566 240131 0.004044409257816854 0.09345035136930102