BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174010.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 = 4,609,908 number of mapped reads = 4,476,801 (97.11%) number of supplementary alignments = 473,268 (10.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,242,714 number of mapped paired reads (second in pair) = 2,234,087 number of mapped paired reads (both in pair) = 4,386,944 number of mapped paired reads (singletons) = 89,857 number of mapped bases = 526,151,471 bp number of sequenced bases = 525,848,723 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,394,150 duplication rate = 63.56% >>>>>>> Insert size mean insert size = 1,004,997.6719 std insert size = 9,024,699.7506 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 52.5829 >>>>>>> ACTG content number of A's = 159,121,741 bp (30.26%) number of C's = 101,989,340 bp (19.4%) number of T's = 158,729,559 bp (30.19%) number of G's = 106,001,758 bp (20.16%) number of N's = 6,325 bp (0%) GC percentage = 39.55% >>>>>>> Mismatches and indels general error rate = 0.011 number of mismatches = 5,633,681 number of insertions = 56,563 mapped reads with insertion percentage = 1.22% number of deletions = 121,889 mapped reads with deletion percentage = 2.66% homopolymer indels = 42.4% >>>>>>> Coverage mean coverageData = 0.17X std coverageData = 2.6085X There is a 3.81% of reference with a coverageData >= 1X There is a 2.96% of reference with a coverageData >= 2X There is a 2.23% of reference with a coverageData >= 3X There is a 1.79% of reference with a coverageData >= 4X There is a 1.33% of reference with a coverageData >= 5X There is a 1.05% of reference with a coverageData >= 6X There is a 0.76% of reference with a coverageData >= 7X There is a 0.61% of reference with a coverageData >= 8X There is a 0.43% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.26% of reference with a coverageData >= 11X There is a 0.22% of reference with a coverageData >= 12X There is a 0.16% of reference with a coverageData >= 13X There is a 0.14% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% 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 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 48990462 0.1965510128057013 1.590332772467159 chr2 243199373 40029084 0.16459369736944182 7.598289180653859 chr3 198022430 33867565 0.17102893343950987 1.1543814634242142 chr4 191154276 33555025 0.17553897146407543 1.4797755360201954 chr5 180915260 25786254 0.14253222199166615 1.0468266262917063 chr6 171115067 26756709 0.15636676225595025 1.1280479890432584 chr7 159138663 41811413 0.2627357312911445 2.622187143341922 chr8 146364022 46919160 0.3205648448223157 1.9428073465747602 chr9 141213431 18651349 0.13207914337836604 1.3070288365582365 chr10 135534747 24948258 0.18407278245777078 3.2968777754795804 chr11 135006516 22379008 0.16576242882973144 1.1744862593139513 chr12 133851895 20817850 0.15552898970911094 1.0870380236251986 chr13 115169878 13641039 0.11844276677969565 0.9541910624574554 chr14 107349540 15546958 0.14482556702152613 1.0524579241191545 chr15 102531392 14612359 0.1425159525777237 1.0273998093077599 chr16 90354753 12383046 0.13704919319518255 1.4230706192892044 chr17 81195210 12117259 0.149236131047632 1.1739116237369656 chr18 78077248 9607786 0.12305487508985972 1.6079437675245454 chr19 59128983 8236521 0.13929752520857663 1.2943300164559948 chr20 63025520 20652808 0.3276896089076298 1.5941416234879697 chr21 48129895 6620291 0.1375504974610894 1.1221456413369397 chr22 51304566 5572758 0.10862109232149045 0.8623972278611397 chrMT 16571 1507218 90.95516263351638 63.466044798893215 chrX 155270560 20066851 0.1292379637195873 0.9955236344219195 chrY 59373566 1074440 0.018096268632407896 0.7640037792652613