BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438288.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 693,577,926 number of mapped reads = 689,680,768 (99.44%) number of supplementary alignments = 18,121,796 (2.61%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 345,072,609 number of mapped paired reads (second in pair) = 344,608,159 number of mapped paired reads (both in pair) = 687,295,544 number of mapped paired reads (singletons) = 2,385,224 number of mapped bases = 97,593,265,260 bp number of sequenced bases = 97,562,215,159 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 281,632,869 duplication rate = 36% >>>>>>> Insert size mean insert size = 109,880.9901 std insert size = 3,224,664.711 median insert size = 480 >>>>>>> Mapping quality mean mapping quality = 54.22 >>>>>>> ACTG content number of A's = 29,970,945,645 bp (30.72%) number of C's = 18,495,675,959 bp (18.96%) number of T's = 28,215,727,458 bp (28.92%) number of G's = 20,879,687,272 bp (21.4%) number of N's = 178,825 bp (0%) GC percentage = 40.36% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 543,072,472 number of insertions = 12,856,939 mapped reads with insertion percentage = 1.82% number of deletions = 11,447,090 mapped reads with deletion percentage = 1.61% homopolymer indels = 47.91% >>>>>>> Coverage mean coverageData = 31.5255X std coverageData = 133.1108X There is a 90.78% of reference with a coverageData >= 1X There is a 89.94% of reference with a coverageData >= 2X There is a 89.04% of reference with a coverageData >= 3X There is a 88.06% of reference with a coverageData >= 4X There is a 87% of reference with a coverageData >= 5X There is a 85.84% of reference with a coverageData >= 6X There is a 84.58% of reference with a coverageData >= 7X There is a 83.22% of reference with a coverageData >= 8X There is a 81.77% of reference with a coverageData >= 9X There is a 80.23% of reference with a coverageData >= 10X There is a 78.61% of reference with a coverageData >= 11X There is a 76.92% of reference with a coverageData >= 12X There is a 75.16% of reference with a coverageData >= 13X There is a 73.35% of reference with a coverageData >= 14X There is a 71.49% of reference with a coverageData >= 15X There is a 69.6% of reference with a coverageData >= 16X There is a 67.67% of reference with a coverageData >= 17X There is a 65.73% of reference with a coverageData >= 18X There is a 63.78% of reference with a coverageData >= 19X There is a 61.83% of reference with a coverageData >= 20X There is a 59.88% of reference with a coverageData >= 21X There is a 57.94% of reference with a coverageData >= 22X There is a 56.02% of reference with a coverageData >= 23X There is a 54.12% of reference with a coverageData >= 24X There is a 52.24% of reference with a coverageData >= 25X There is a 50.4% of reference with a coverageData >= 26X There is a 48.58% of reference with a coverageData >= 27X There is a 46.81% of reference with a coverageData >= 28X There is a 45.08% of reference with a coverageData >= 29X There is a 43.38% of reference with a coverageData >= 30X There is a 41.74% of reference with a coverageData >= 31X There is a 40.13% of reference with a coverageData >= 32X There is a 38.58% of reference with a coverageData >= 33X There is a 37.06% of reference with a coverageData >= 34X There is a 35.6% of reference with a coverageData >= 35X There is a 34.18% of reference with a coverageData >= 36X There is a 32.81% of reference with a coverageData >= 37X There is a 31.49% of reference with a coverageData >= 38X There is a 30.21% of reference with a coverageData >= 39X There is a 28.98% of reference with a coverageData >= 40X There is a 27.79% of reference with a coverageData >= 41X There is a 26.65% of reference with a coverageData >= 42X There is a 25.55% of reference with a coverageData >= 43X There is a 24.49% of reference with a coverageData >= 44X There is a 23.47% of reference with a coverageData >= 45X There is a 22.49% of reference with a coverageData >= 46X There is a 21.55% of reference with a coverageData >= 47X There is a 20.65% of reference with a coverageData >= 48X There is a 19.78% of reference with a coverageData >= 49X There is a 18.95% of reference with a coverageData >= 50X There is a 18.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7532940806 30.222355217321606 42.00967832611724 chr2 243199373 8431203958 34.66786881066507 320.1325096716269 chr3 198022430 6884707406 34.76731098593225 26.051426893175492 chr4 191154276 6786929384 35.504983336077714 36.67271437438601 chr5 180915260 6284780592 34.73880861128022 26.48977329683209 chr6 171115067 5878379128 34.3533695253148 33.68807850601521 chr7 159138663 5190438909 32.61582579087019 29.625130254883675 chr8 146364022 5029710054 34.364388087121576 29.542496649706013 chr9 141213431 4213147262 29.83531546655785 53.35908178771597 chr10 135534747 4352953235 32.11688021965319 86.90058243076976 chr11 135006516 4410736614 32.670546168304945 29.114780084626457 chr12 133851895 4429861670 33.09524807250581 27.820889622543255 chr13 115169878 3374651230 29.301509115083025 26.79571508291761 chr14 107349540 2957419403 27.549437128468366 27.42645715815094 chr15 102531392 2675154923 26.091081675746683 26.243530589462107 chr16 90354753 2570194945 28.445597599054917 89.94112663415261 chr17 81195210 2162433068 26.632520169601136 45.95905032013738 chr18 78077248 2638586085 33.794557986982326 63.75052843653638 chr19 59128983 1308782724 22.134368926994735 30.00988070733705 chr20 63025520 1870662882 29.681038442840297 30.587642939920613 chr21 48129895 1267320336 26.331250795373645 42.320835166701336 chr22 51304566 870164705 16.960765343965683 23.734927751672757 chrMT 16571 604543576 36482.021362621446 13139.303985114175 chrX 155270560 5740302903 36.969679912276995 29.55946520310407 chrY 59373566 127259462 2.143369020482954 36.364607040755445