BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174033.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 3,245,416 number of mapped reads = 3,160,113 (97.37%) number of supplementary alignments = 292,366 (9.01%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,580,479 number of mapped paired reads (second in pair) = 1,579,634 number of mapped paired reads (both in pair) = 3,101,586 number of mapped paired reads (singletons) = 58,527 number of mapped bases = 373,401,253 bp number of sequenced bases = 373,206,976 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,402,599 duplication rate = 64.12% >>>>>>> Insert size mean insert size = 939,449.7974 std insert size = 9,103,399.0793 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 52.8073 >>>>>>> ACTG content number of A's = 112,744,276 bp (30.21%) number of C's = 72,896,785 bp (19.53%) number of T's = 112,478,344 bp (30.14%) number of G's = 75,083,041 bp (20.12%) number of N's = 4,530 bp (0%) GC percentage = 39.65% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 3,929,594 number of insertions = 38,930 mapped reads with insertion percentage = 1.19% number of deletions = 78,546 mapped reads with deletion percentage = 2.43% homopolymer indels = 43.61% >>>>>>> Coverage mean coverageData = 0.1206X std coverageData = 1.9631X There is a 2.6% of reference with a coverageData >= 1X There is a 2.05% of reference with a coverageData >= 2X There is a 1.56% of reference with a coverageData >= 3X There is a 1.28% of reference with a coverageData >= 4X There is a 0.96% of reference with a coverageData >= 5X There is a 0.77% of reference with a coverageData >= 6X There is a 0.56% of reference with a coverageData >= 7X There is a 0.45% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.27% of reference with a coverageData >= 10X There is a 0.19% of reference with a coverageData >= 11X There is a 0.17% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% 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 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 31401042 0.12598180046259544 1.738576547086229 chr2 243199373 39634740 0.16297221292589434 5.31692313649585 chr3 198022430 26374814 0.1331910430550721 1.0332838962160134 chr4 191154276 22734704 0.11893379774564918 1.1286026958667739 chr5 180915260 27674575 0.15296982134066522 1.1033879542682674 chr6 171115067 22830625 0.13342264594385483 1.0558509697978538 chr7 159138663 27684294 0.1739633441560333 2.4456308679210492 chr8 146364022 16351065 0.11171505658678879 1.1207012171126052 chr9 141213431 14064263 0.09959578844876306 1.083814210030617 chr10 135534747 14736183 0.10872623682250279 2.126622263946648 chr11 135006516 17206058 0.12744613008160288 1.0178613477018514 chr12 133851895 12383425 0.09251587360791567 0.862958830128856 chr13 115169878 11984391 0.10405838061233337 0.9183611946694247 chr14 107349540 11018796 0.10264409144184503 0.9062590042924374 chr15 102531392 10913748 0.10644299065012207 0.9073678908312326 chr16 90354753 14279669 0.15804004245354975 1.5614532184422596 chr17 81195210 8172964 0.10065820385217306 1.0530632448012829 chr18 78077248 5481825 0.0702102743170456 1.3747533911166394 chr19 59128983 6133434 0.1037297394409777 1.8025776018028024 chr20 63025520 9744648 0.154614321309844 1.1057565515358343 chr21 48129895 5467868 0.11360648096157284 0.96503887473663 chr22 51304566 2976390 0.05801413464836638 0.6477247963943985 chrMT 16571 1011652 61.04954438476857 49.93808505043649 chrX 155270560 12599760 0.0811471279552286 0.8026105229778796 chrY 59373566 540320 0.009100346103516841 0.4602517511401482