BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716705.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,446,343 number of mapped reads = 2,182,078 (89.2%) number of supplementary alignments = 8,732 (0.36%) number of secondary alignments = 0 number of mapped bases = 124,255,593 bp number of sequenced bases = 124,218,508 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 68,389 duplication rate = 2.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5352 >>>>>>> ACTG content number of A's = 32,498,288 bp (26.16%) number of C's = 26,246,818 bp (21.13%) number of T's = 37,094,634 bp (29.86%) number of G's = 28,377,803 bp (22.85%) number of N's = 965 bp (0%) GC percentage = 43.97% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 640,792 number of insertions = 9,595 mapped reads with insertion percentage = 0.44% number of deletions = 23,256 mapped reads with deletion percentage = 1.06% homopolymer indels = 39.96% >>>>>>> Coverage mean coverageData = 0.0401X std coverageData = 0.3102X There is a 3.52% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 10468051 0.04199809395861044 0.41473640792611655 chr2 243199373 9661023 0.039724703566567175 0.443223966378599 chr3 198022430 7217047 0.036445603662171 0.21846528890500266 chr4 191154276 7426516 0.03885090177109091 0.23735363794934897 chr5 180915260 7214806 0.03987947727571461 0.22095550354661403 chr6 171115067 6629207 0.03874122317937087 0.26690767316808767 chr7 159138663 7014596 0.0440785153511061 0.46553714588685896 chr8 146364022 6411481 0.043805034272698516 0.3129698949726874 chr9 141213431 4128731 0.029237523447751934 0.23072111131214595 chr10 135534747 5394069 0.03979842158114627 0.38545545065025744 chr11 135006516 4384997 0.03247989156315981 0.25843090317553813 chr12 133851895 6280335 0.04692003053075939 0.24301057994693198 chr13 115169878 3642831 0.03163006736883059 0.19777807291182256 chr14 107349540 4067244 0.03788785680870174 0.23126811109428547 chr15 102531392 5365951 0.05233471325542913 0.2643803110330991 chr16 90354753 4213915 0.046637446953122656 0.2593739274491082 chr17 81195210 5451017 0.06713471151808093 0.31021210098978425 chr18 78077248 2305683 0.029530792376288674 0.371213851965329 chr19 59128983 3215079 0.05437399456033262 0.3942294480212355 chr20 63025520 3965043 0.06291170624216984 0.29845634964719253 chr21 48129895 1498716 0.03113898336989931 0.21432329771631553 chr22 51304566 1124386 0.021915905106769638 0.16666983152867365 chrMT 16571 60320 3.640094140365699 3.084841818812357 chrX 155270560 6744860 0.04343940023144117 0.2500987116676909 chrY 59373566 369689 0.0062264914322309696 0.1729493960913787