BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438267.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 = 773,454,946 number of mapped reads = 771,000,221 (99.68%) number of supplementary alignments = 13,257,529 (1.71%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 385,621,342 number of mapped paired reads (second in pair) = 385,378,879 number of mapped paired reads (both in pair) = 769,260,312 number of mapped paired reads (singletons) = 1,739,909 number of mapped bases = 111,395,019,663 bp number of sequenced bases = 111,364,312,714 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 382,860,649 duplication rate = 46.7% >>>>>>> Insert size mean insert size = 41,055.4969 std insert size = 1,951,214.8453 median insert size = 241 >>>>>>> Mapping quality mean mapping quality = 55.0497 >>>>>>> ACTG content number of A's = 33,723,182,714 bp (30.28%) number of C's = 22,226,887,112 bp (19.96%) number of T's = 32,205,450,063 bp (28.92%) number of G's = 23,208,110,001 bp (20.84%) number of N's = 682,824 bp (0%) GC percentage = 40.8% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 561,573,008 number of insertions = 13,981,249 mapped reads with insertion percentage = 1.79% number of deletions = 12,415,359 mapped reads with deletion percentage = 1.58% homopolymer indels = 48.51% >>>>>>> Coverage mean coverageData = 35.9839X std coverageData = 63.5809X There is a 88.64% of reference with a coverageData >= 1X There is a 87.66% of reference with a coverageData >= 2X There is a 86.61% of reference with a coverageData >= 3X There is a 85.57% of reference with a coverageData >= 4X There is a 84.44% of reference with a coverageData >= 5X There is a 83.27% of reference with a coverageData >= 6X There is a 82.02% of reference with a coverageData >= 7X There is a 80.72% of reference with a coverageData >= 8X There is a 79.36% of reference with a coverageData >= 9X There is a 77.96% of reference with a coverageData >= 10X There is a 76.51% of reference with a coverageData >= 11X There is a 75.02% of reference with a coverageData >= 12X There is a 73.5% of reference with a coverageData >= 13X There is a 71.96% of reference with a coverageData >= 14X There is a 70.4% of reference with a coverageData >= 15X There is a 68.82% of reference with a coverageData >= 16X There is a 67.24% of reference with a coverageData >= 17X There is a 65.65% of reference with a coverageData >= 18X There is a 64.07% of reference with a coverageData >= 19X There is a 62.49% of reference with a coverageData >= 20X There is a 60.91% of reference with a coverageData >= 21X There is a 59.35% of reference with a coverageData >= 22X There is a 57.8% of reference with a coverageData >= 23X There is a 56.27% of reference with a coverageData >= 24X There is a 54.75% of reference with a coverageData >= 25X There is a 53.26% of reference with a coverageData >= 26X There is a 51.79% of reference with a coverageData >= 27X There is a 50.34% of reference with a coverageData >= 28X There is a 48.92% of reference with a coverageData >= 29X There is a 47.52% of reference with a coverageData >= 30X There is a 46.15% of reference with a coverageData >= 31X There is a 44.81% of reference with a coverageData >= 32X There is a 43.49% of reference with a coverageData >= 33X There is a 42.21% of reference with a coverageData >= 34X There is a 40.95% of reference with a coverageData >= 35X There is a 39.72% of reference with a coverageData >= 36X There is a 38.53% of reference with a coverageData >= 37X There is a 37.36% of reference with a coverageData >= 38X There is a 36.22% of reference with a coverageData >= 39X There is a 35.12% of reference with a coverageData >= 40X There is a 34.04% of reference with a coverageData >= 41X There is a 32.99% of reference with a coverageData >= 42X There is a 31.97% of reference with a coverageData >= 43X There is a 30.98% of reference with a coverageData >= 44X There is a 30.01% of reference with a coverageData >= 45X There is a 29.07% of reference with a coverageData >= 46X There is a 28.16% of reference with a coverageData >= 47X There is a 27.28% of reference with a coverageData >= 48X There is a 26.42% of reference with a coverageData >= 49X There is a 25.59% of reference with a coverageData >= 50X There is a 24.78% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9151111348 36.71449768624649 37.004745701290446 chr2 243199373 10151697139 41.742283352844005 122.87470590327165 chr3 198022430 8210939845 41.46469591853812 48.51921386090989 chr4 191154276 7457438027 39.012666538518864 33.122654257360864 chr5 180915260 7489816318 41.39958297602977 35.43518891084889 chr6 171115067 7044783788 41.169862546353095 35.95348086942437 chr7 159138663 6168167273 38.75970274426649 35.1884909772715 chr8 146364022 5534171548 37.81101033148706 33.829308419302926 chr9 141213431 4525759364 32.04907162123977 37.153182534090895 chr10 135534747 5824718939 42.975835111862494 44.599669899463485 chr11 135006516 5877385798 43.534089850892826 37.804934003224375 chr12 133851895 5793679601 43.28425534057624 36.423646031567856 chr13 115169878 3412450057 29.629709749280103 31.350781800238785 chr14 107349540 3206284639 29.8677072952525 33.465830691506056 chr15 102531392 3041667087 29.665715325507332 35.36528633567048 chr16 90354753 2462701238 27.255912458750235 43.7822139340342 chr17 81195210 2797790467 34.45758028090573 38.08618243642106 chr18 78077248 3038038362 38.91067423380496 35.7570957931888 chr19 59128983 1790432839 30.28012233865074 58.14124068925937 chr20 63025520 2004365995 31.802450737415572 35.289260305474265 chr21 48129895 1567614173 32.57048811346877 39.64187536266465 chr22 51304566 1157356547 22.558548628985577 31.252574505184178 chrMT 16571 261120483 15757.678052018588 6178.075706126006 chrX 155270560 2962996402 19.082795875792552 23.03591581530357 chrY 59373566 462532386 7.790207278437681 24.204850402631926