BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751216.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 5,885,229 number of mapped reads = 3,686,836 (62.65%) number of supplementary alignments = 212,473 (3.61%) number of secondary alignments = 0 number of mapped bases = 362,725,364 bp number of sequenced bases = 362,602,099 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 136,509 duplication rate = 1.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.0561 >>>>>>> ACTG content number of A's = 107,572,691 bp (29.67%) number of C's = 73,693,287 bp (20.32%) number of T's = 108,321,212 bp (29.87%) number of G's = 73,012,312 bp (20.14%) number of N's = 2,597 bp (0%) GC percentage = 40.46% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 1,421,425 number of insertions = 286,837 mapped reads with insertion percentage = 7.43% number of deletions = 55,531 mapped reads with deletion percentage = 1.47% homopolymer indels = 53.48% >>>>>>> Coverage mean coverageData = 0.1172X std coverageData = 1.3364X There is a 9.26% of reference with a coverageData >= 1X There is a 1.62% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 42694236 0.1712903896837232 3.7473947344065004 chr2 243199373 27885162 0.1146596788306687 0.5972071804776586 chr3 198022430 23724650 0.11980789246955509 0.49774854587161504 chr4 191154276 17519975 0.09165358665583813 0.460752738920557 chr5 180915260 29703326 0.16418364045133615 0.5410398432931857 chr6 171115067 20206074 0.11808471547394479 0.7423898450305036 chr7 159138663 20532615 0.12902342279952422 0.8124551804631456 chr8 146364022 18087569 0.12357933837046375 0.6324756370379386 chr9 141213431 15920561 0.11274112446145437 0.6552781126172702 chr10 135534747 18361479 0.13547432969347706 2.045620885040374 chr11 135006516 16296887 0.12071185512260757 0.6693965487917084 chr12 133851895 19097751 0.1426782265577936 0.4800589743698199 chr13 115169878 10723935 0.09311406060532598 0.35689805625910265 chr14 107349540 7632835 0.07110263350918877 0.3295728528581763 chr15 102531392 8684232 0.084698274651338 0.3395243841723882 chr16 90354753 10274581 0.11371378548287327 1.042623772025671 chr17 81195210 9476947 0.11671805516606214 0.6093532718008997 chr18 78077248 7745823 0.09920717236345215 1.3353561403584322 chr19 59128983 6371102 0.1077492234222936 2.5186636381265575 chr20 63025520 6049833 0.0959902115841329 0.3843834439858338 chr21 48129895 4592769 0.09542445500868016 0.4177387491146433 chr22 51304566 3719743 0.07250315693149027 0.3178029212412152 chrMT 16571 880527 53.13662422304025 24.642042821891497 chrX 155270560 15548265 0.10013659382693023 0.4358118055197636 chrY 59373566 994487 0.01674965926756025 0.7058660021737747