BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013235.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 = 1,858,666 number of mapped reads = 1,661,617 (89.4%) number of supplementary alignments = 16,607 (0.89%) number of secondary alignments = 0 number of mapped bases = 112,451,074 bp number of sequenced bases = 112,407,495 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 124,152 duplication rate = 5.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0391 >>>>>>> ACTG content number of A's = 31,700,996 bp (28.2%) number of C's = 20,630,604 bp (18.35%) number of T's = 35,971,678 bp (32%) number of G's = 24,079,133 bp (21.42%) number of N's = 25,084 bp (0.02%) GC percentage = 39.77% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 890,465 number of insertions = 8,711 mapped reads with insertion percentage = 0.52% number of deletions = 24,972 mapped reads with deletion percentage = 1.49% homopolymer indels = 47.45% >>>>>>> Coverage mean coverageData = 0.0363X std coverageData = 0.3996X There is a 2.69% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% 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 8129623 0.03261625976049223 0.6441730126286154 chr2 243199373 9893095 0.04067894944778497 0.43129133296279204 chr3 198022430 6065523 0.030630484637523134 0.22329847554574855 chr4 191154276 8570349 0.044834722922965115 0.2953243937151716 chr5 180915260 7082311 0.03914711782742926 0.2539714121100865 chr6 171115067 6692458 0.03911086333502122 0.2848268308137915 chr7 159138663 6747514 0.04240021797845568 0.6074765138334364 chr8 146364022 6030801 0.0412041218708789 0.6987299860841014 chr9 141213431 4578445 0.0324221638662685 0.35531760299215187 chr10 135534747 5257430 0.038790274201788266 0.35918083148348323 chr11 135006516 4986531 0.03693548391397642 0.30386103051962526 chr12 133851895 4813986 0.03596501939699845 0.24784259717116733 chr13 115169878 3694413 0.03207794489458433 0.22835070472485924 chr14 107349540 3785295 0.035261399350197495 0.25197707723791707 chr15 102531392 3207833 0.03128634984298272 0.22355332154696594 chr16 90354753 3100690 0.03431684440551788 0.26943174345702 chr17 81195210 2704490 0.033308491966459595 0.25828449629808037 chr18 78077248 3065734 0.03926539521474937 0.7070519689785387 chr19 59128983 1917886 0.03243563313104844 0.47006868086541775 chr20 63025520 2189661 0.03474245035979076 0.24325903113110373 chr21 48129895 1525530 0.03169610072907909 0.24691618359642936 chr22 51304566 1167206 0.022750528676141614 0.1871034011350768 chrMT 16571 125259 7.5589282481443485 5.304861970109317 chrX 155270560 6792437 0.043745813758899306 0.2991281204567845 chrY 59373566 326574 0.00550032652578085 0.15783236068781906