BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068165.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 = 1,715,891 number of mapped reads = 1,598,389 (93.15%) number of supplementary alignments = 9,494 (0.55%) number of secondary alignments = 0 number of mapped bases = 109,767,772 bp number of sequenced bases = 109,722,629 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,068 duplication rate = 3.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1986 >>>>>>> ACTG content number of A's = 32,051,713 bp (29.21%) number of C's = 20,948,557 bp (19.09%) number of T's = 33,884,478 bp (30.88%) number of G's = 22,708,914 bp (20.7%) number of N's = 128,967 bp (0.12%) GC percentage = 39.79% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 914,060 number of insertions = 7,408 mapped reads with insertion percentage = 0.46% number of deletions = 25,481 mapped reads with deletion percentage = 1.58% homopolymer indels = 47.88% >>>>>>> Coverage mean coverageData = 0.0355X std coverageData = 0.3765X There is a 2.82% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 11775891 0.04724518218953605 0.9366310603569876 chr2 243199373 11471848 0.047170549243151214 0.35775148519216804 chr3 198022430 14913809 0.07531373592375369 0.33414116816143 chr4 191154276 4815886 0.02519371316600838 0.19837654596710655 chr5 180915260 1385867 0.007660310136358868 0.11010234459746142 chr6 171115067 4023586 0.02351392002201653 0.23316212232829445 chr7 159138663 928319 0.005833397004221407 0.11251866262765665 chr8 146364022 6958045 0.047539312632444604 0.2918274220602457 chr9 141213431 5277881 0.037375205478861286 0.31016073376502135 chr10 135534747 6195731 0.04571322953810509 0.3786832415174063 chr11 135006516 2786254 0.020637922394797597 0.18249029846699605 chr12 133851895 643143 0.00480488528010754 0.09550028152966118 chr13 115169878 6854209 0.05951390345312339 0.2933570522282785 chr14 107349540 4836345 0.04505231228750491 0.27056854851576695 chr15 102531392 5030113 0.04905924811788374 0.2648083902678053 chr16 90354753 2619055 0.028986355593269123 0.23563156064531243 chr17 81195210 1347539 0.016596286899190234 0.1536663590592035 chr18 78077248 761428 0.009752239218267528 0.4061738425781593 chr19 59128983 1596555 0.02700122543964607 0.5662257958540184 chr20 63025520 3296460 0.05230357480588815 0.2809465974574908 chr21 48129895 376044 0.007813106594144865 0.1385808322748087 chr22 51304566 579337 0.011292113844214177 0.1247094731689319 chrMT 16571 4387 0.2647396053346207 0.5687105935950332 chrX 155270560 10988588 0.07077058265262906 0.36871411769519064 chrY 59373566 301452 0.005077208938401982 0.17069596262205383