BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714105.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 = 549,590 number of mapped reads = 471,597 (85.81%) number of supplementary alignments = 20,904 (3.8%) number of secondary alignments = 0 number of mapped bases = 58,776,255 bp number of sequenced bases = 57,694,423 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 463,461 duplication rate = 34.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 36.1332 >>>>>>> ACTG content number of A's = 16,576,260 bp (28.73%) number of C's = 11,624,327 bp (20.15%) number of T's = 15,770,055 bp (27.33%) number of G's = 13,723,346 bp (23.79%) number of N's = 435 bp (0%) GC percentage = 43.93% >>>>>>> Mismatches and indels general error rate = 0.038 number of mismatches = 2,084,636 number of insertions = 51,607 mapped reads with insertion percentage = 10.58% number of deletions = 180,735 mapped reads with deletion percentage = 36.55% homopolymer indels = 28.04% >>>>>>> Coverage mean coverageData = 0.019X std coverageData = 19.2574X There is a 0.03% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% 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 0.01% 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 11549671 0.04633758164237432 36.04205267454413 chr2 243199373 5564781 0.022881559813889816 11.425095964925546 chr3 198022430 1693515 0.008552137250310482 5.931056017431561 chr4 191154276 3801209 0.01988555568592146 16.32112113676853 chr5 180915260 793516 0.004386119777845163 1.7465368432185269 chr6 171115067 192542 0.0011252194407871752 0.2567548903200515 chr7 159138663 1128731 0.007092751558431781 2.428960554342547 chr8 146364022 457417 0.003125201082544725 0.662409667667129 chr9 141213431 1971561 0.013961568570626968 10.157265384659722 chr10 135534747 14388355 0.1061598986125676 46.6682962037826 chr11 135006516 1121490 0.008306932385396865 4.541014843668267 chr12 133851895 10702609 0.07995859154627583 54.922789879265565 chr13 115169878 2663266 0.023124675012679966 11.491213401454768 chr14 107349540 219691 0.0020465015499833536 0.9792527816876512 chr15 102531392 170317 0.0016611205278477055 0.4033510143120717 chr16 90354753 451369 0.004995520268867317 2.107967291547574 chr17 81195210 564932 0.006957701076208806 3.0333312454981063 chr18 78077248 184231 0.002359599047343472 0.627967696299273 chr19 59128983 43080 7.285767116948384E-4 0.1088589358838627 chr20 63025520 145325 0.0023058119948871506 0.8380591279577296 chr21 48129895 80143 0.0016651397224116114 0.43468221561616655 chr22 51304566 97585 0.0019020724198310147 0.5642241506335278 chrMT 16571 119579 7.2161607627783475 59.64570341069326 chrX 155270560 567203 0.0036529977092888697 0.6835967238435005 chrY 59373566 104137 0.0017539286759363586 0.7101031036940565