BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234038.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 = 2,246,459 number of mapped reads = 1,800,567 (80.15%) number of supplementary alignments = 14,439 (0.64%) number of secondary alignments = 0 number of mapped bases = 120,914,847 bp number of sequenced bases = 120,834,216 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,551 duplication rate = 3.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2726 >>>>>>> ACTG content number of A's = 34,698,859 bp (28.72%) number of C's = 21,175,131 bp (17.52%) number of T's = 39,693,522 bp (32.85%) number of G's = 25,241,138 bp (20.89%) number of N's = 25,566 bp (0.02%) GC percentage = 38.41% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,015,483 number of insertions = 9,673 mapped reads with insertion percentage = 0.53% number of deletions = 45,628 mapped reads with deletion percentage = 2.49% homopolymer indels = 44.74% >>>>>>> Coverage mean coverageData = 0.0391X std coverageData = 0.4272X There is a 3.05% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% 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 10721822 0.043016229837196676 0.916529204878738 chr2 243199373 7374765 0.030323947422348 0.3456917894076266 chr3 198022430 12470236 0.06297385604246954 0.311171870676723 chr4 191154276 6539201 0.034209022873231465 0.23939934801061957 chr5 180915260 7600973 0.0420139959448418 0.25020519409738695 chr6 171115067 10600285 0.06194828536051709 0.47687803876077717 chr7 159138663 7730406 0.04857654233277051 0.45529328030353494 chr8 146364022 7763617 0.0530432062054157 0.7949270233537764 chr9 141213431 5077448 0.03595584332201376 0.288936417558026 chr10 135534747 4599048 0.033932612129345695 0.3462589248012804 chr11 135006516 2259950 0.016739562407491502 0.19351459667913357 chr12 133851895 3204563 0.023941110434036066 0.19229072652008483 chr13 115169878 6204823 0.05387539787096067 0.2854253159804226 chr14 107349540 5368693 0.050011327482167134 0.28399470952828154 chr15 102531392 1772694 0.017289280535662678 0.16000783599891133 chr16 90354753 1992086 0.022047384712567362 0.20798706149579718 chr17 81195210 2184877 0.026908939579071228 0.22798407942888002 chr18 78077248 4253290 0.05447540876440727 0.5222249442504358 chr19 59128983 2376491 0.04019164341115084 0.4829264326110781 chr20 63025520 1941878 0.030810979425477173 0.2195390964822423 chr21 48129895 2015031 0.041866515603244094 0.259689971378786 chr22 51304566 513285 0.010004665081856457 0.11708915148742974 chrMT 16571 20974 1.2657051475469192 1.5316547786834127 chrX 155270560 6052381 0.03897957861425888 0.2580894354662568 chrY 59373566 276030 0.004649038597412189 0.11935948558734079