BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714047.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 250,452 number of mapped reads = 220,944 (88.22%) number of supplementary alignments = 7,089 (2.83%) number of secondary alignments = 0 number of mapped bases = 28,675,416 bp number of sequenced bases = 28,040,989 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 184,580 duplication rate = 42.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.383 >>>>>>> ACTG content number of A's = 7,499,042 bp (26.74%) number of C's = 6,305,954 bp (22.49%) number of T's = 7,097,502 bp (25.31%) number of G's = 7,138,213 bp (25.46%) number of N's = 278 bp (0%) GC percentage = 47.94% >>>>>>> Mismatches and indels general error rate = 0.044 number of mismatches = 1,151,073 number of insertions = 30,144 mapped reads with insertion percentage = 13.17% number of deletions = 101,747 mapped reads with deletion percentage = 43.77% homopolymer indels = 30.18% >>>>>>> Coverage mean coverageData = 0.0093X std coverageData = 2.5385X There is a 0.04% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0.02% 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 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 2458534 0.009863702606381872 2.477548671224521 chr2 243199373 3252205 0.013372587930150627 3.8306020510908914 chr3 198022430 903715 0.004563700182853023 0.9206188695119788 chr4 191154276 945183 0.0049446081969937205 0.9238854142596841 chr5 180915260 1358423 0.007508614806733274 1.7231706276935639 chr6 171115067 1016963 0.005943152860992656 1.2016103552425157 chr7 159138663 835404 0.005249535117685386 1.0735862348542176 chr8 146364022 1388797 0.009488650154749095 1.953801232230072 chr9 141213431 1073751 0.007603745567232907 2.0204876314805515 chr10 135534747 1359956 0.010034002572048922 1.4975201744253068 chr11 135006516 1649404 0.012217217723031975 2.0172444923933193 chr12 133851895 1849195 0.013815232126523126 3.6006017602999383 chr13 115169878 787184 0.0068349816260116205 2.239381006107585 chr14 107349540 1700127 0.0158373012124691 8.00329978898017 chr15 102531392 953987 0.00930434066475953 1.5961574376551226 chr16 90354753 513620 0.005684482364751747 0.6920591251326923 chr17 81195210 1090636 0.013432270204116721 2.720665418318799 chr18 78077248 898336 0.011505733398800122 2.474943371365574 chr19 59128983 743368 0.012571973375561016 1.3493587250056591 chr20 63025520 878295 0.013935545474277722 2.3014590289385053 chr21 48129895 239217 0.004970237313004735 0.9103193050216049 chr22 51304566 154239 0.0030063406052396975 0.34450792614304676 chrMT 16571 85107 5.135900066381027 44.42065829765638 chrX 155270560 2297076 0.014794021480955566 1.626318533495121 chrY 59373566 242694 0.004087576616166191 1.0017854808915165