BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013259.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 = 2,202,184 number of mapped reads = 1,588,994 (72.16%) number of supplementary alignments = 11,741 (0.53%) number of secondary alignments = 0 number of mapped bases = 97,200,794 bp number of sequenced bases = 97,164,859 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 134,372 duplication rate = 6.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3276 >>>>>>> ACTG content number of A's = 28,870,197 bp (29.71%) number of C's = 18,768,688 bp (19.32%) number of T's = 28,912,760 bp (29.76%) number of G's = 20,612,308 bp (21.21%) number of N's = 906 bp (0%) GC percentage = 40.53% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 750,532 number of insertions = 6,415 mapped reads with insertion percentage = 0.4% number of deletions = 21,867 mapped reads with deletion percentage = 1.36% homopolymer indels = 45.04% >>>>>>> Coverage mean coverageData = 0.0314X std coverageData = 0.3788X There is a 1.93% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 7678509 0.030806378612793908 0.48216269026821174 chr2 243199373 6527065 0.026838329883358703 0.3347219175633662 chr3 198022430 6208285 0.0313514231695874 0.29345364044632427 chr4 191154276 6669864 0.034892570229504045 0.2854608859831027 chr5 180915260 4055289 0.02241540597515102 0.22639800742067254 chr6 171115067 4338900 0.025356621576754546 0.25040473079604947 chr7 159138663 8075333 0.05074400430271304 0.7525757390488075 chr8 146364022 4012402 0.027413854478527518 0.4580545815012689 chr9 141213431 3364765 0.023827513970678893 0.29535659309094336 chr10 135534747 6926019 0.05110142714915755 0.38219691835336195 chr11 135006516 8366763 0.06197303099059308 0.6317515650502307 chr12 133851895 3385973 0.025296414369030785 0.24134118131503302 chr13 115169878 2295856 0.01993451794747929 0.2120430060377122 chr14 107349540 2362506 0.022007602454561053 0.22773575270649998 chr15 102531392 2532698 0.024701683558533957 0.24311244262529455 chr16 90354753 2999960 0.03320201650044907 0.28267203875586977 chr17 81195210 2753661 0.033914081877490065 0.35553309438527525 chr18 78077248 2250848 0.0288284751019913 0.5059669347270065 chr19 59128983 2024121 0.03423229856667753 0.37520467697841253 chr20 63025520 1600661 0.02539702964767288 0.24085555869396286 chr21 48129895 1970680 0.040945030110703544 0.313592951617987 chr22 51304566 2175890 0.042411234898663795 0.3737905723035518 chrMT 16571 21302 1.2854987628990404 2.054288568547652 chrX 155270560 4360627 0.028084055341849736 0.2843402341108557 chrY 59373566 242817 0.00408964824514667 0.10301410889682261