BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237323.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 = 3,373,913 number of mapped reads = 2,912,223 (86.32%) number of supplementary alignments = 33,877 (1%) number of secondary alignments = 0 number of mapped bases = 177,831,835 bp number of sequenced bases = 177,746,044 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,193,382 duplication rate = 21.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7453 >>>>>>> ACTG content number of A's = 45,737,551 bp (25.73%) number of C's = 31,096,630 bp (17.49%) number of T's = 59,285,520 bp (33.35%) number of G's = 41,607,615 bp (23.41%) number of N's = 18,728 bp (0.01%) GC percentage = 40.9% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 1,052,347 number of insertions = 13,203 mapped reads with insertion percentage = 0.45% number of deletions = 48,485 mapped reads with deletion percentage = 1.64% homopolymer indels = 41.77% >>>>>>> Coverage mean coverageData = 0.0574X std coverageData = 0.9746X There is a 1.44% of reference with a coverageData >= 1X There is a 0.89% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.54% of reference with a coverageData >= 4X There is a 0.43% of reference with a coverageData >= 5X There is a 0.34% of reference with a coverageData >= 6X There is a 0.27% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.17% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% 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 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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 19919589 0.07991791121756121 1.0218921855464074 chr2 243199373 22348080 0.09189201322488606 1.775388782952513 chr3 198022430 4317851 0.02180485816682484 0.42770371176713573 chr4 191154276 19563157 0.10234224109116973 1.0387170952205491 chr5 180915260 17000423 0.09396898304764341 0.8880282898995886 chr6 171115067 12840344 0.07503923660912923 0.9772517367385697 chr7 159138663 8316787 0.05226125972919604 0.739171475626282 chr8 146364022 7849927 0.05363290030387386 0.800616437480001 chr9 141213431 13731889 0.09724208882085728 0.9354856136291716 chr10 135534747 5831325 0.043024575830727746 1.0233341108872833 chr11 135006516 3307029 0.024495328803240873 0.4880688034762399 chr12 133851895 4252637 0.031771212503192425 0.5280303214209169 chr13 115169878 9089920 0.07892619283663738 0.8843029792187351 chr14 107349540 4925389 0.04588178952606597 0.6520507302118621 chr15 102531392 2765574 0.02697294892865592 0.5192893164210932 chr16 90354753 2181445 0.02414311286977897 0.4847641164454265 chr17 81195210 3928132 0.04837886372853768 0.6505638741364201 chr18 78077248 3532031 0.045237647208057334 2.5081593387538725 chr19 59128983 1699028 0.028734267254351388 0.6124010646937549 chr20 63025520 2112338 0.03351559812596548 0.5650872780641591 chr21 48129895 1792916 0.03725160838185913 0.6410704753609139 chr22 51304566 984002 0.019179618437859897 0.41294740348175385 chrMT 16571 18452 1.1135115563333535 3.7665789195669364 chrX 155270560 4911223 0.031630097811201296 0.5213285404609679 chrY 59373566 612347 0.01031346171796385 0.6292092156662732