BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068961.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 = 1,977,447 number of mapped reads = 1,458,150 (73.74%) number of supplementary alignments = 6,582 (0.33%) number of secondary alignments = 0 number of mapped bases = 90,557,384 bp number of sequenced bases = 90,506,280 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,313 duplication rate = 3.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0941 >>>>>>> ACTG content number of A's = 23,036,095 bp (25.45%) number of C's = 15,015,314 bp (16.59%) number of T's = 30,379,545 bp (33.57%) number of G's = 21,874,068 bp (24.17%) number of N's = 201,258 bp (0.22%) GC percentage = 40.76% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 914,709 number of insertions = 8,568 mapped reads with insertion percentage = 0.58% number of deletions = 31,745 mapped reads with deletion percentage = 2.15% homopolymer indels = 49% >>>>>>> Coverage mean coverageData = 0.0293X std coverageData = 0.3641X There is a 2.47% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.06% 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 11595004 0.046519458822130676 0.7242051257190479 chr2 243199373 7392262 0.030395892509147218 0.3713200640497233 chr3 198022430 5344256 0.026988134626971298 0.19876536271396483 chr4 191154276 6715814 0.03513295198272206 0.23909755070824165 chr5 180915260 5996190 0.03314363862948874 0.21196181520605645 chr6 171115067 4256542 0.024875319716878 0.2453410081586783 chr7 159138663 4557295 0.02863725831352498 0.48434178055185123 chr8 146364022 5457937 0.03729015454358039 0.3856714985776031 chr9 141213431 4542980 0.032171019200007964 0.43341168201997765 chr10 135534747 3726009 0.027491171691935205 0.4171834502678477 chr11 135006516 3473794 0.025730565478780297 0.2923713260035503 chr12 133851895 4544448 0.033951316116966446 0.22511308507951594 chr13 115169878 1905528 0.016545367878222465 0.14900593989383895 chr14 107349540 1995252 0.018586497902086958 0.23669490284982972 chr15 102531392 1643129 0.016025618768542613 0.1592179756364406 chr16 90354753 1984994 0.021968894099018785 0.2009288348930187 chr17 81195210 2311812 0.028472270716462213 0.23336737580007366 chr18 78077248 1540444 0.019729742523711902 0.5470976512410872 chr19 59128983 1601409 0.027083317161061268 0.5294397365277299 chr20 63025520 1480344 0.023488009301628927 0.19852658964372563 chr21 48129895 1115189 0.023170401680701776 0.1956522655419277 chr22 51304566 936302 0.01824987662891447 0.1513878655556339 chrMT 16571 60694 3.662663689578179 3.8650633963828147 chrX 155270560 6113269 0.03937171991908833 0.3116233433460039 chrY 59373566 266487 0.004488310505048661 0.12114055471381692