BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525005.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,237,512 number of mapped reads = 1,128,372 (91.18%) number of supplementary alignments = 4,272 (0.35%) number of secondary alignments = 0 number of mapped bases = 64,837,482 bp number of sequenced bases = 64,816,712 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,445 duplication rate = 2.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2334 >>>>>>> ACTG content number of A's = 16,197,181 bp (24.99%) number of C's = 12,622,186 bp (19.47%) number of T's = 20,349,236 bp (31.4%) number of G's = 15,647,414 bp (24.14%) number of N's = 695 bp (0%) GC percentage = 43.61% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 326,027 number of insertions = 3,468 mapped reads with insertion percentage = 0.31% number of deletions = 12,606 mapped reads with deletion percentage = 1.11% homopolymer indels = 44.63% >>>>>>> Coverage mean coverageData = 0.0209X std coverageData = 0.2069X There is a 1.94% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 6863911 0.027538190165632526 0.3736628699995118 chr2 243199373 6075781 0.02498271654672399 0.24356251572731735 chr3 198022430 3533212 0.0178424838034762 0.14319951260088729 chr4 191154276 4056529 0.021221230750809884 0.16437420809408523 chr5 180915260 2762730 0.015270851115599646 0.13364602208262144 chr6 171115067 4308588 0.02517947762016772 0.21714347617411264 chr7 159138663 4085220 0.025670820170205905 0.2625665215469225 chr8 146364022 3795234 0.025930101866153965 0.20553227440225313 chr9 141213431 1798955 0.012739262740525014 0.1585825853282384 chr10 135534747 3278293 0.02418784166100225 0.20743973092842752 chr11 135006516 2730284 0.020223349812241654 0.18515650507586723 chr12 133851895 3495244 0.026112771881190027 0.17211041624752232 chr13 115169878 1757163 0.015257140413051406 0.13176886156146755 chr14 107349540 1464101 0.013638633197683008 0.1275498806223361 chr15 102531392 1818021 0.017731359777110996 0.14545953478704685 chr16 90354753 2076151 0.0229777729567807 0.16662764825511134 chr17 81195210 1698492 0.020918623155232925 0.191823007373952 chr18 78077248 1273839 0.016315111413762944 0.2350239766905534 chr19 59128983 1613912 0.027294770146816156 0.24368372037580963 chr20 63025520 1592162 0.025262179510775952 0.16982964292748484 chr21 48129895 940570 0.01954232395478943 0.15274027925745468 chr22 51304566 905264 0.017644901235496273 0.14032630689606396 chrMT 16571 19495 1.176452839297568 1.3440440883582627 chrX 155270560 2712017 0.017466395432591986 0.15901690664231338 chrY 59373566 182314 0.0030706257394073314 0.08461242754580271