BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238662.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 = 2,353,792 number of mapped reads = 2,139,215 (90.88%) number of supplementary alignments = 15,934 (0.68%) number of secondary alignments = 0 number of mapped bases = 131,355,333 bp number of sequenced bases = 131,285,571 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 264,456 duplication rate = 10.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8975 >>>>>>> ACTG content number of A's = 32,895,490 bp (25.06%) number of C's = 22,854,338 bp (17.41%) number of T's = 43,949,962 bp (33.48%) number of G's = 31,579,211 bp (24.05%) number of N's = 6,570 bp (0.01%) GC percentage = 41.46% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 770,190 number of insertions = 8,494 mapped reads with insertion percentage = 0.39% number of deletions = 39,714 mapped reads with deletion percentage = 1.84% homopolymer indels = 42.11% >>>>>>> Coverage mean coverageData = 0.0424X std coverageData = 0.4476X There is a 3.26% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% 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 11315254 0.04539709451716872 0.630009958957945 chr2 243199373 8895135 0.03657548492117206 0.8341090520996732 chr3 198022430 8175012 0.04128326270917895 0.2564116223496175 chr4 191154276 9003286 0.04709957939941663 0.2819561048210558 chr5 180915260 6221280 0.03438781228294396 0.23432451701431048 chr6 171115067 10315290 0.06028276867051106 0.45196614120826684 chr7 159138663 8740031 0.05492085226328689 0.5333453813491712 chr8 146364022 6153198 0.04204037246257144 0.5757056263916647 chr9 141213431 3492404 0.02473138691743847 0.3119082685975758 chr10 135534747 6681035 0.04929389066554276 0.3791704872103184 chr11 135006516 5120161 0.037925287991284806 0.3016453796220178 chr12 133851895 5261472 0.039308162204203384 0.2545710538200326 chr13 115169878 5249551 0.04558093740448349 0.30620463854821217 chr14 107349540 3519142 0.03278208737550249 0.2440777189905071 chr15 102531392 4577684 0.04464665806936475 0.3078697418136697 chr16 90354753 4468168 0.049451388572773806 0.3189457695823426 chr17 81195210 3150735 0.038804444252314885 0.26334019563788824 chr18 78077248 2852750 0.036537532675331996 0.779230834063727 chr19 59128983 2750779 0.04652166941548783 0.46849906123268303 chr20 63025520 3132488 0.04970189853253095 0.2907934250046811 chr21 48129895 2188838 0.045477722317906574 0.2808004414717761 chr22 51304566 1777566 0.034647325542135954 0.23173380179080608 chrMT 16571 12395 0.747993482590067 1.0884376148605373 chrX 155270560 7903468 0.050901265507125114 0.3007919558385569 chrY 59373566 398211 0.006706873560533655 0.20810813192431943