BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524810.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 = 1,785,950 number of mapped reads = 1,609,633 (90.13%) number of supplementary alignments = 5,625 (0.31%) number of secondary alignments = 0 number of mapped bases = 91,397,883 bp number of sequenced bases = 91,369,049 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,740 duplication rate = 2.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4612 >>>>>>> ACTG content number of A's = 22,588,903 bp (24.72%) number of C's = 16,683,808 bp (18.26%) number of T's = 29,812,622 bp (32.63%) number of G's = 22,272,814 bp (24.38%) number of N's = 10,902 bp (0.01%) GC percentage = 42.64% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 470,813 number of insertions = 5,983 mapped reads with insertion percentage = 0.37% number of deletions = 17,896 mapped reads with deletion percentage = 1.1% homopolymer indels = 41.8% >>>>>>> Coverage mean coverageData = 0.0295X std coverageData = 0.255X There is a 2.62% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 7236318 0.029032296774097105 0.3230488438836502 chr2 243199373 7712136 0.03171116728166894 0.4152317400674717 chr3 198022430 6111304 0.030861675619272017 0.19731454613346486 chr4 191154276 5775032 0.030211367073996295 0.21816493307829615 chr5 180915260 5442112 0.030081000353425133 0.19122387647456496 chr6 171115067 5229968 0.030564041447034 0.21357324106525352 chr7 159138663 5036147 0.03164628195977743 0.3168357153422689 chr8 146364022 4575980 0.03126437725249174 0.23068331744349424 chr9 141213431 3861838 0.02734752617121809 0.2260015000854421 chr10 135534747 4473928 0.033009454025837374 0.30448383062423934 chr11 135006516 4099117 0.030362364139520495 0.2299704272486836 chr12 133851895 4153557 0.031030991380435816 0.19646260005798538 chr13 115169878 2888296 0.025078571325741962 0.175718948301115 chr14 107349540 2687966 0.025039380699721676 0.1797883072002543 chr15 102531392 2642160 0.02576927854446763 0.17973700305155954 chr16 90354753 2740573 0.030331254405620477 0.21288655379751165 chr17 81195210 2613983 0.03219380798448578 0.20830629077297633 chr18 78077248 2392891 0.030647737481730913 0.3443060313666337 chr19 59128983 1980688 0.03349775185546486 0.2822696703910709 chr20 63025520 1947065 0.030893279420780663 0.20192352980683673 chr21 48129895 1203319 0.025001488160321148 0.18889404862646017 chr22 51304566 1124248 0.021913215287699735 0.16446533199428987 chrMT 16571 21420 1.2926196367147427 1.3152815186964655 chrX 155270560 5145373 0.03313811066309028 0.21962123119134966 chrY 59373566 302464 0.005094253560582836 0.1333683392914662