BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234144.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 = 1,955,921 number of mapped reads = 619,167 (31.66%) number of supplementary alignments = 6,349 (0.32%) number of secondary alignments = 0 number of mapped bases = 39,955,215 bp number of sequenced bases = 39,937,283 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,457 duplication rate = 10.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2472 >>>>>>> ACTG content number of A's = 11,242,267 bp (28.15%) number of C's = 6,963,434 bp (17.44%) number of T's = 13,142,587 bp (32.91%) number of G's = 8,572,866 bp (21.47%) number of N's = 16,129 bp (0.04%) GC percentage = 38.9% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 341,524 number of insertions = 4,052 mapped reads with insertion percentage = 0.64% number of deletions = 10,368 mapped reads with deletion percentage = 1.65% homopolymer indels = 43.63% >>>>>>> Coverage mean coverageData = 0.0129X std coverageData = 0.234X There is a 0.66% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 3122520 0.012527631776692746 0.33378004640307923 chr2 243199373 3408402 0.014014846987290547 0.23446181476917288 chr3 198022430 2745493 0.013864555646549736 0.21303097560225148 chr4 191154276 2428152 0.01270257747203102 0.2060460016619929 chr5 180915260 2418451 0.01336786625959579 0.21145815541679602 chr6 171115067 3270318 0.019111806209326967 0.2624464393510147 chr7 159138663 2316141 0.014554231865074799 0.2616038535168055 chr8 146364022 2329789 0.015917771103611787 0.3315327745080277 chr9 141213431 1336417 0.00946380943042167 0.17498038600043186 chr10 135534747 1959216 0.01445545178167485 0.2271191992351096 chr11 135006516 1650677 0.012226646897546782 0.20641227391366684 chr12 133851895 2036089 0.015211506717928798 0.2242867192947961 chr13 115169878 1225915 0.010644406517474995 0.20370233930318885 chr14 107349540 1057624 0.009852152137773483 0.1815113181628844 chr15 102531392 1037366 0.010117545268477385 0.1804808132085925 chr16 90354753 1023211 0.011324373826798021 0.184095920473719 chr17 81195210 892641 0.0109937642873268 0.18759326082917996 chr18 78077248 1075945 0.013780519005997752 0.29009713442432444 chr19 59128983 693249 0.011724351829288186 0.24295986248643853 chr20 63025520 773852 0.012278391356390236 0.19866490754530175 chr21 48129895 465525 0.009672262945929967 0.17327461664528931 chr22 51304566 396904 0.007736231508127366 0.14680935610552218 chrMT 16571 18292 1.1038561342103674 1.5890886203668384 chrX 155270560 2108385 0.01357878145090737 0.21881550642890019 chrY 59373566 164641 0.0027729680241877336 0.08635783836819984