BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237868.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 = 2,589,999 number of mapped reads = 1,960,535 (75.7%) number of supplementary alignments = 11,796 (0.46%) number of secondary alignments = 0 number of mapped bases = 122,941,186 bp number of sequenced bases = 122,893,678 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,946 duplication rate = 3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6931 >>>>>>> ACTG content number of A's = 34,132,529 bp (27.77%) number of C's = 22,324,019 bp (18.17%) number of T's = 38,987,807 bp (31.72%) number of G's = 27,339,077 bp (22.25%) number of N's = 110,246 bp (0.09%) GC percentage = 40.41% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 976,131 number of insertions = 9,946 mapped reads with insertion percentage = 0.5% number of deletions = 29,682 mapped reads with deletion percentage = 1.5% homopolymer indels = 46.48% >>>>>>> Coverage mean coverageData = 0.0397X std coverageData = 0.3828X There is a 3.41% of reference with a coverageData >= 1X There is a 0.39% 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 7562622 0.03034143694269873 0.454544608117602 chr2 243199373 12156786 0.04998691341198482 0.5174897821215396 chr3 198022430 6741736 0.03404531496760241 0.2098288506216032 chr4 191154276 10471127 0.05477840840976008 0.2703269531814046 chr5 180915260 6811718 0.037651428630177466 0.22015292813648352 chr6 171115067 13807853 0.08069337926858305 0.5558941929585662 chr7 159138663 7710008 0.048448364807488674 0.6824313165283155 chr8 146364022 5583843 0.0381503796062669 0.3817751330985882 chr9 141213431 3823643 0.027077049066246396 0.375240531049959 chr10 135534747 6889847 0.0508345435580442 0.3544846994003638 chr11 135006516 6013241 0.044540376110439 0.3823759766454044 chr12 133851895 4194486 0.03133676964379174 0.20640876674408812 chr13 115169878 2935255 0.025486308147343872 0.1777728853810775 chr14 107349540 4116569 0.03834733711946973 0.24564386765878962 chr15 102531392 2087442 0.020359052571918657 0.16125524999374755 chr16 90354753 3674639 0.04066901715729332 0.25350488354776596 chr17 81195210 2322883 0.028608621124324943 0.3156740004372258 chr18 78077248 4625652 0.05924455739013752 0.7384602243152597 chr19 59128983 2098065 0.0354828527999543 0.3523462321910111 chr20 63025520 2080846 0.03301592751634576 0.21377753787068832 chr21 48129895 1392922 0.02894089006427294 0.20874336640718988 chr22 51304566 1048639 0.020439486809029826 0.15840430010561893 chrMT 16571 17758 1.071631162874902 1.3887466606801013 chrX 155270560 4488642 0.028908519425704396 0.26037708615937166 chrY 59373566 284964 0.004799509599945538 0.11111978335009237