BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238254.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 = 3,097,748 number of mapped reads = 2,846,245 (91.88%) number of supplementary alignments = 22,722 (0.73%) number of secondary alignments = 0 number of mapped bases = 189,806,906 bp number of sequenced bases = 189,722,588 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 117,060 duplication rate = 3.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.84 >>>>>>> ACTG content number of A's = 52,152,968 bp (27.49%) number of C's = 36,685,047 bp (19.34%) number of T's = 57,878,745 bp (30.51%) number of G's = 42,949,331 bp (22.64%) number of N's = 56,497 bp (0.03%) GC percentage = 41.97% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,648,766 number of insertions = 15,409 mapped reads with insertion percentage = 0.54% number of deletions = 51,269 mapped reads with deletion percentage = 1.78% homopolymer indels = 45.67% >>>>>>> Coverage mean coverageData = 0.0613X std coverageData = 0.4896X There is a 5.01% of reference with a coverageData >= 1X There is a 0.79% 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 0.01% 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 15409637 0.06182386602759959 0.7939625437322874 chr2 243199373 16177365 0.06651894205335801 0.6797645159339494 chr3 198022430 12252883 0.06187623795950792 0.29302151060146997 chr4 191154276 12344811 0.06458035497986976 0.33276045525774295 chr5 180915260 11925959 0.06592013852231149 0.30487374868458783 chr6 171115067 10684426 0.06244000710936811 0.35435026965913213 chr7 159138663 9950418 0.06252671608784346 0.7559801897797583 chr8 146364022 9273525 0.06335932063960363 0.5385604347052725 chr9 141213431 8570471 0.0606916136751893 0.4976812326516261 chr10 135534747 9204555 0.06791287993476684 0.4770367946881696 chr11 135006516 8484733 0.06284684066656457 0.41478791986768127 chr12 133851895 8896187 0.06646291410368153 0.31802994611243723 chr13 115169878 5349113 0.046445416917086604 0.253497558493853 chr14 107349540 4761639 0.044356398732588884 0.3068477777052567 chr15 102531392 5968404 0.05821050395960683 0.2897197537293537 chr16 90354753 5733716 0.06345782385128096 0.3414022963179927 chr17 81195210 5374102 0.06618742657356265 0.35207666887284483 chr18 78077248 5415583 0.0693618581433608 0.8524517862564299 chr19 59128983 4205382 0.07112217708868762 0.5841675608210851 chr20 63025520 4049990 0.06425952534782736 0.30873593305852726 chr21 48129895 2523421 0.052429389260043056 0.3130126256824576 chr22 51304566 2268663 0.04421951449701377 0.24827773190533936 chrMT 16571 8618 0.5200651740993302 0.767853258884991 chrX 155270560 10515341 0.06772269643388934 0.35657350978733576 chrY 59373566 457964 0.007713264182245681 0.2017396976799457