BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548922.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 7,632,633 number of mapped reads = 6,675,684 (87.46%) number of secondary alignments = 0 number of mapped bases = 264,556,140 bp number of sequenced bases = 264,527,959 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 205,079 duplication rate = 2.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5407 >>>>>>> ACTG content number of A's = 78,589,758 bp (29.71%) number of C's = 53,670,904 bp (20.29%) number of T's = 78,733,584 bp (29.76%) number of G's = 53,531,238 bp (20.24%) number of N's = 2,475 bp (0%) GC percentage = 40.53% >>>>>>> Mismatches and indels general error rate = 0.0027 number of mismatches = 705,044 number of insertions = 7,834 mapped reads with insertion percentage = 0.12% number of deletions = 21,276 mapped reads with deletion percentage = 0.32% homopolymer indels = 42.4% >>>>>>> Coverage mean coverageData = 0.0855X std coverageData = 0.9317X There is a 7.14% of reference with a coverageData >= 1X There is a 1.05% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.04% 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% 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 20633449 0.08278193617820515 0.8897520292079097 chr2 243199373 22425800 0.09221158641720675 0.49706855230425545 chr3 198022430 18110462 0.09145661933347651 0.348294473549605 chr4 191154276 17835063 0.09330193063533666 0.360715270248977 chr5 180915260 16718060 0.0924082357673974 0.35618098166576034 chr6 171115067 15599788 0.09116548456834604 0.38808134609134126 chr7 159138663 14682676 0.09226341181463867 0.697712644130634 chr8 146364022 13939120 0.09523597267639994 3.638959063866867 chr9 141213431 11079855 0.07846176473114658 0.47485921423073235 chr10 135534747 12108206 0.08933654481975754 0.4456882491243149 chr11 135006516 11963613 0.08861507840110473 0.5325297961204049 chr12 133851895 12092845 0.09034496672609678 0.3600241477379065 chr13 115169878 8787858 0.07630344107857785 0.315241056957643 chr14 107349540 8186952 0.0762644348545881 0.3747474388903139 chr15 102531392 7448456 0.07264561472061161 0.3082827215249329 chr16 90354753 6993058 0.0773955743091899 0.34890255525737396 chr17 81195210 6578022 0.08101490223376477 0.352280554451602 chr18 78077248 7136203 0.0913992639699596 0.865486600151593 chr19 59128983 4755751 0.08043011664854781 0.7935820557485628 chr20 63025520 5150451 0.08172008735509044 0.33684997776129777 chr21 48129895 3373448 0.07009049157493487 0.3365049770711063 chr22 51304566 2729060 0.05319331616605041 0.2939928248370019 chrMT 16571 9731 0.5872307042423511 0.9296235737962318 chrX 155270560 15441611 0.09944970250638627 0.43517293379402305 chrY 59373566 776602 0.013079928532505527 0.17877664901799561