BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714174.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 = 1,149,386 number of mapped reads = 888,240 (77.28%) number of supplementary alignments = 30,702 (2.67%) number of secondary alignments = 0 number of mapped bases = 114,645,706 bp number of sequenced bases = 112,486,257 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 777,797 duplication rate = 44.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.5249 >>>>>>> ACTG content number of A's = 31,071,118 bp (27.62%) number of C's = 24,327,284 bp (21.63%) number of T's = 29,555,938 bp (26.28%) number of G's = 27,531,186 bp (24.48%) number of N's = 731 bp (0%) GC percentage = 46.1% >>>>>>> Mismatches and indels general error rate = 0.0415 number of mismatches = 4,268,387 number of insertions = 123,908 mapped reads with insertion percentage = 13.48% number of deletions = 373,002 mapped reads with deletion percentage = 40.09% homopolymer indels = 28.47% >>>>>>> Coverage mean coverageData = 0.037X std coverageData = 4.854X There is a 0.08% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 11485097 0.04607850906818804 5.4019478233663865 chr2 243199373 11878417 0.04884230108603117 10.077276326251233 chr3 198022430 5662848 0.028597002874876345 3.0155658722303498 chr4 191154276 4771792 0.02496304084769728 2.7523408363611135 chr5 180915260 6019136 0.0332704714903541 3.4941700153385575 chr6 171115067 4451271 0.02601332003101749 2.7275230061902542 chr7 159138663 4774858 0.030004386803224557 3.3563670002604327 chr8 146364022 5026358 0.034341485915165684 4.220315331606584 chr9 141213431 4232296 0.02997091685988424 3.5750265561180568 chr10 135534747 5982762 0.04414190554397095 4.548169175629281 chr11 135006516 5481060 0.04059848489090705 4.152757247698087 chr12 133851895 4866054 0.03635401650458516 4.171242173409783 chr13 115169878 2771072 0.024060735742031436 2.904750219302584 chr14 107349540 3731534 0.034760596086392176 3.894570236359672 chr15 102531392 3610628 0.03521485400295746 3.5623435039793625 chr16 90354753 3986275 0.04411804434903386 5.302482993796352 chr17 81195210 4870793 0.05998867420873719 6.262376400709781 chr18 78077248 2327882 0.029815113360552873 2.902610112153431 chr19 59128983 2785357 0.04710645877335654 5.302334250803592 chr20 63025520 2956352 0.04690722107489157 3.881934646364045 chr21 48129895 945327 0.019641160654931825 2.056315751854473 chr22 51304566 1586121 0.030915786325918827 3.4858356608506074 chrMT 16571 940249 56.74063122322129 520.4649317733179 chrX 155270560 9100527 0.058610769485213425 3.805182255254707 chrY 59373566 401640 0.00676462653430653 0.9893403343071758