BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438280.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 = 705,171,500 number of mapped reads = 702,961,073 (99.69%) number of supplementary alignments = 11,009,744 (1.56%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 351,500,433 number of mapped paired reads (second in pair) = 351,460,640 number of mapped paired reads (both in pair) = 701,421,586 number of mapped paired reads (singletons) = 1,539,487 number of mapped bases = 100,880,023,561 bp number of sequenced bases = 100,853,198,189 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 377,075,734 duplication rate = 50.81% >>>>>>> Insert size mean insert size = 37,435.0951 std insert size = 1,874,937.1538 median insert size = 225 >>>>>>> Mapping quality mean mapping quality = 55.0705 >>>>>>> ACTG content number of A's = 30,518,178,542 bp (30.26%) number of C's = 20,146,070,644 bp (19.98%) number of T's = 29,222,445,984 bp (28.98%) number of G's = 20,965,879,826 bp (20.79%) number of N's = 623,193 bp (0%) GC percentage = 40.76% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 513,691,917 number of insertions = 12,411,716 mapped reads with insertion percentage = 1.74% number of deletions = 11,048,265 mapped reads with deletion percentage = 1.55% homopolymer indels = 48.24% >>>>>>> Coverage mean coverageData = 32.5872X std coverageData = 72.7164X There is a 90.57% of reference with a coverageData >= 1X There is a 89.73% of reference with a coverageData >= 2X There is a 88.77% of reference with a coverageData >= 3X There is a 87.79% of reference with a coverageData >= 4X There is a 86.67% of reference with a coverageData >= 5X There is a 85.5% of reference with a coverageData >= 6X There is a 84.22% of reference with a coverageData >= 7X There is a 82.87% of reference with a coverageData >= 8X There is a 81.44% of reference with a coverageData >= 9X There is a 79.95% of reference with a coverageData >= 10X There is a 78.39% of reference with a coverageData >= 11X There is a 76.78% of reference with a coverageData >= 12X There is a 75.13% of reference with a coverageData >= 13X There is a 73.43% of reference with a coverageData >= 14X There is a 71.7% of reference with a coverageData >= 15X There is a 69.95% of reference with a coverageData >= 16X There is a 68.18% of reference with a coverageData >= 17X There is a 66.39% of reference with a coverageData >= 18X There is a 64.6% of reference with a coverageData >= 19X There is a 62.8% of reference with a coverageData >= 20X There is a 61.01% of reference with a coverageData >= 21X There is a 59.22% of reference with a coverageData >= 22X There is a 57.44% of reference with a coverageData >= 23X There is a 55.69% of reference with a coverageData >= 24X There is a 53.95% of reference with a coverageData >= 25X There is a 52.23% of reference with a coverageData >= 26X There is a 50.54% of reference with a coverageData >= 27X There is a 48.88% of reference with a coverageData >= 28X There is a 47.24% of reference with a coverageData >= 29X There is a 45.64% of reference with a coverageData >= 30X There is a 44.08% of reference with a coverageData >= 31X There is a 42.54% of reference with a coverageData >= 32X There is a 41.05% of reference with a coverageData >= 33X There is a 39.59% of reference with a coverageData >= 34X There is a 38.16% of reference with a coverageData >= 35X There is a 36.78% of reference with a coverageData >= 36X There is a 35.43% of reference with a coverageData >= 37X There is a 34.12% of reference with a coverageData >= 38X There is a 32.85% of reference with a coverageData >= 39X There is a 31.62% of reference with a coverageData >= 40X There is a 30.43% of reference with a coverageData >= 41X There is a 29.27% of reference with a coverageData >= 42X There is a 28.15% of reference with a coverageData >= 43X There is a 27.07% of reference with a coverageData >= 44X There is a 26.02% of reference with a coverageData >= 45X There is a 25.01% of reference with a coverageData >= 46X There is a 24.04% of reference with a coverageData >= 47X There is a 23.09% of reference with a coverageData >= 48X There is a 22.19% of reference with a coverageData >= 49X There is a 21.31% of reference with a coverageData >= 50X There is a 20.46% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8120434657 32.57939588844595 31.119972865501264 chr2 243199373 9025421816 37.111205118115166 132.86513480208336 chr3 198022430 7440355800 37.573298135973786 162.78708145155315 chr4 191154276 6736878902 35.243150417414675 28.07499106938196 chr5 180915260 6298568598 34.815021120938056 32.433557297827136 chr6 171115067 6119514190 35.76256782811534 28.552051892990608 chr7 159138663 5599037229 35.18338738965024 29.817185111705044 chr8 146364022 5347161917 36.53330814453842 28.35541638546495 chr9 141213431 4500870965 31.872824936885785 34.89900863535126 chr10 135534747 4936135004 36.41970131836377 36.34039602105285 chr11 135006516 4763784151 35.28558688974686 28.845454196346633 chr12 133851895 4811359016 35.94539334687791 28.276968472667082 chr13 115169878 3477380606 30.193490402065027 27.487150400868316 chr14 107349540 3197027962 29.78147798304492 29.810994319484937 chr15 102531392 2884505116 28.132897249654036 30.294569700963013 chr16 90354753 2787585344 30.85156288347111 51.22126518749434 chr17 81195210 2441833933 30.07362051283567 37.047184007709326 chr18 78077248 2756176937 35.300641449350266 28.72699565293844 chr19 59128983 1564120164 26.4526816569803 241.9112924526097 chr20 63025520 2199735102 34.902291992196176 31.745116551533457 chr21 48129895 1342499179 27.893249694394722 72.44613909842685 chr22 51304566 1106254771 21.56250129861736 28.74729330563634 chrMT 16571 86524259 5221.426528272283 2065.970869361179 chrX 155270560 2847004308 18.335763766164042 26.4551977881644 chrY 59373566 489853635 8.250365743570127 25.947110046148296