BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231884.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 = 6,522,705 number of mapped reads = 2,141,402 (32.83%) number of supplementary alignments = 14,912 (0.23%) number of secondary alignments = 0 number of mapped bases = 136,967,045 bp number of sequenced bases = 136,921,865 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,356 duplication rate = 2.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.4621 >>>>>>> ACTG content number of A's = 38,947,538 bp (28.45%) number of C's = 27,940,014 bp (20.41%) number of T's = 36,522,308 bp (26.67%) number of G's = 33,502,639 bp (24.47%) number of N's = 9,366 bp (0.01%) GC percentage = 44.87% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 957,518 number of insertions = 11,745 mapped reads with insertion percentage = 0.54% number of deletions = 28,265 mapped reads with deletion percentage = 1.31% homopolymer indels = 42.52% >>>>>>> Coverage mean coverageData = 0.0442X std coverageData = 6.7822X There is a 3.82% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 12077543 0.0484554178904132 0.9612791467987606 chr2 243199373 13958780 0.057396447317321006 24.144325168767086 chr3 198022430 9451146 0.0477276538824415 0.23951068489264465 chr4 191154276 5737153 0.03001320776104428 0.21994322040198316 chr5 180915260 8221745 0.045445281951340094 0.2365865586143784 chr6 171115067 12340325 0.07211711520412167 0.4797455704183712 chr7 159138663 8346487 0.05244788942332637 0.7793454728840912 chr8 146364022 4059744 0.027737308284682148 0.2999189846464271 chr9 141213431 4350586 0.030808585055907323 0.3205256798311461 chr10 135534747 6742475 0.04974720615371053 0.5125065786018178 chr11 135006516 6943412 0.05143019911720409 0.45011544806311476 chr12 133851895 5180526 0.03870341917833887 0.21825818357403848 chr13 115169878 5207015 0.045211604721852705 0.22819454923390076 chr14 107349540 6617711 0.06164638432544751 0.3702500099611473 chr15 102531392 2746303 0.02678499673543884 0.1785528305415417 chr16 90354753 2429531 0.02688880130080152 0.2357603154253362 chr17 81195210 4953951 0.061012847925388705 0.3581503835078655 chr18 78077248 1488937 0.019070049702571486 0.7948321883671824 chr19 59128983 4189933 0.07086090082083772 0.6013281218214507 chr20 63025520 3853465 0.0611413440142977 0.2890696389926284 chr21 48129895 2281353 0.04739991641369672 0.25701051091159727 chr22 51304566 986481 0.01922793772390551 0.14855493559358282 chrMT 16571 23583 1.4231488745398588 1.6679282082990012 chrX 155270560 4432051 0.028544052394736 0.23713872170790878 chrY 59373566 346809 0.005841134756837748 0.1370704716981101