BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013204.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 = 1,959,692 number of mapped reads = 1,727,015 (88.13%) number of supplementary alignments = 13,105 (0.67%) number of secondary alignments = 0 number of mapped bases = 115,478,443 bp number of sequenced bases = 115,434,758 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,900 duplication rate = 3.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1187 >>>>>>> ACTG content number of A's = 32,091,148 bp (27.8%) number of C's = 21,092,256 bp (18.27%) number of T's = 36,950,698 bp (32.01%) number of G's = 25,275,953 bp (21.9%) number of N's = 24,703 bp (0.02%) GC percentage = 40.17% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 893,066 number of insertions = 8,111 mapped reads with insertion percentage = 0.47% number of deletions = 25,166 mapped reads with deletion percentage = 1.44% homopolymer indels = 47.44% >>>>>>> Coverage mean coverageData = 0.0373X std coverageData = 0.3663X There is a 3.1% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.08% 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 7167821 0.028757485021471622 0.5208675451837657 chr2 243199373 14767590 0.060722154904568774 0.44176055009689563 chr3 198022430 9645715 0.048710214292391016 0.25489981537306583 chr4 191154276 10866240 0.056845393298970724 0.2850693623084953 chr5 180915260 5180443 0.028634638117315255 0.197127810510954 chr6 171115067 5280934 0.030861887807927514 0.23819977179722837 chr7 159138663 7118954 0.04473428308242102 0.7136428033467432 chr8 146364022 8127569 0.055529828225135816 0.5577230967187129 chr9 141213431 2981560 0.02111385566433833 0.27181223705290175 chr10 135534747 3120566 0.023024103184403334 0.23324231555941155 chr11 135006516 5472273 0.04053339914349023 0.26514318315784485 chr12 133851895 3118098 0.02329513526872369 0.18397574960477936 chr13 115169878 2568934 0.022305606679552097 0.17367536744599193 chr14 107349540 3143564 0.02928344173621983 0.2130769816767587 chr15 102531392 3824438 0.037300166567523045 0.22640318781832314 chr16 90354753 1986940 0.021990431427553126 0.1855318979070443 chr17 81195210 3847964 0.047391514844287 0.26385296818987536 chr18 78077248 1602865 0.020529219984802744 0.44419889224916687 chr19 59128983 2156600 0.036472807252578655 0.37606893180034706 chr20 63025520 2500470 0.03967392891006691 0.23580782841329778 chr21 48129895 1553118 0.03226929956942561 0.21437483838018107 chr22 51304566 813258 0.015851571573571054 0.1422579595151508 chrMT 16571 626807 37.8255385915153 19.629157739503466 chrX 155270560 7758791 0.049969491962932315 0.2846456810323228 chrY 59373566 246931 0.00415893833966449 0.09317291307117766