BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234019.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 = 1,561,838 number of mapped reads = 1,183,249 (75.76%) number of supplementary alignments = 16,830 (1.08%) number of secondary alignments = 0 number of mapped bases = 75,963,191 bp number of sequenced bases = 75,913,407 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 140,405 duplication rate = 9.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4383 >>>>>>> ACTG content number of A's = 20,693,145 bp (27.26%) number of C's = 14,070,546 bp (18.53%) number of T's = 24,101,382 bp (31.75%) number of G's = 17,029,791 bp (22.43%) number of N's = 18,543 bp (0.02%) GC percentage = 40.97% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 633,800 number of insertions = 5,979 mapped reads with insertion percentage = 0.5% number of deletions = 28,624 mapped reads with deletion percentage = 2.38% homopolymer indels = 44.1% >>>>>>> Coverage mean coverageData = 0.0245X std coverageData = 0.3116X There is a 1.51% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 7615130 0.030552100409812016 0.4956747169940473 chr2 243199373 3877092 0.01594203123212822 0.3714181518589292 chr3 198022430 6595587 0.0333072723125355 0.27116332818060324 chr4 191154276 3718643 0.01945362184835457 0.21377293179846577 chr5 180915260 4994752 0.027608240454674745 0.24773717786649757 chr6 171115067 6726790 0.0393115002549717 0.3261141326616176 chr7 159138663 4601727 0.028916461363006424 0.33344527581826994 chr8 146364022 3320686 0.022687856992615302 0.46745981888655636 chr9 141213431 3170887 0.022454570911176287 0.257325073352731 chr10 135534747 2500149 0.01844655378299411 0.24704366011895465 chr11 135006516 2920759 0.021634207640763056 0.23512840759715353 chr12 133851895 2570349 0.01920293321211478 0.20677713739477957 chr13 115169878 3037423 0.026373415104251476 0.2491090314460677 chr14 107349540 3197790 0.029788576644110446 0.2607198716230954 chr15 102531392 1646260 0.016056155757643475 0.18603391727663643 chr16 90354753 2003191 0.02217028914903901 0.23689083241361333 chr17 81195210 2211791 0.02724041233466851 0.2479029371343212 chr18 78077248 1127516 0.014441031528160418 0.41526592979825605 chr19 59128983 2227670 0.03767475588071589 0.38485813315942774 chr20 63025520 1803615 0.028617217279603563 0.26581352675002573 chr21 48129895 1654949 0.034385053198225345 0.27828345117868986 chr22 51304566 749926 0.014617139534910012 0.17254357551918656 chrMT 16571 206073 12.43576126968801 10.545797699139756 chrX 155270560 3265300 0.021029743178616733 0.21937797033674825 chrY 59373566 219136 0.003690800717612279 0.10007866643806156