BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063594.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,483,441 number of mapped reads = 2,216,119 (89.24%) number of supplementary alignments = 19,777 (0.8%) number of secondary alignments = 0 number of mapped bases = 148,694,044 bp number of sequenced bases = 148,633,951 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 309,906 duplication rate = 9.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3736 >>>>>>> ACTG content number of A's = 42,042,618 bp (28.29%) number of C's = 27,992,120 bp (18.83%) number of T's = 47,008,388 bp (31.63%) number of G's = 31,586,597 bp (21.25%) number of N's = 4,228 bp (0%) GC percentage = 40.08% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,248,761 number of insertions = 11,371 mapped reads with insertion percentage = 0.51% number of deletions = 33,701 mapped reads with deletion percentage = 1.5% homopolymer indels = 47.04% >>>>>>> Coverage mean coverageData = 0.048X std coverageData = 0.6196X There is a 2.12% of reference with a coverageData >= 1X There is a 1.14% of reference with a coverageData >= 2X There is a 0.65% of reference with a coverageData >= 3X There is a 0.37% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 11509897 0.04617800731577716 0.8721925037004447 chr2 243199373 11997450 0.04933174724920035 0.5617868342333034 chr3 198022430 10075888 0.05088255911211674 0.42073394861696173 chr4 191154276 8032794 0.04202257029290833 0.3909189847569691 chr5 180915260 6397211 0.035360262036491556 0.350403803682724 chr6 171115067 13123917 0.07669644310164692 0.5379701423463514 chr7 159138663 11436340 0.07186399448385462 0.8134517741324099 chr8 146364022 6510096 0.04447879957821875 1.5121151212572785 chr9 141213431 5117352 0.03623842267524822 0.48684461301530196 chr10 135534747 6507000 0.048009828800580565 0.49190211342105994 chr11 135006516 7222610 0.05349823263345304 0.49601332395060105 chr12 133851895 7561091 0.056488486771143584 0.45095365818991556 chr13 115169878 4042459 0.035099967718989857 0.351943130979543 chr14 107349540 2694517 0.02510040564682438 0.3332442267907901 chr15 102531392 3149019 0.03071273039968091 0.3213055988521828 chr16 90354753 3658081 0.040485761717482645 0.38675137611580185 chr17 81195210 4969317 0.06120209554233556 0.459985956798828 chr18 78077248 4864105 0.06229862251292464 0.8548657305134165 chr19 59128983 2890773 0.04888927313361706 0.6725350783293145 chr20 63025520 2412053 0.03827105274180998 0.3754252935748393 chr21 48129895 2399776 0.04986040380931643 0.4236769497843712 chr22 51304566 1680769 0.03276061237902295 0.3197173573778373 chrMT 16571 107976 6.515961619697062 6.111327800186402 chrX 155270560 9886743 0.06367429215171247 0.5142440641964477 chrY 59373566 446810 0.007525402802991486 0.19755730527705437