BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438296.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 = 743,425,010 number of mapped reads = 741,093,010 (99.69%) number of supplementary alignments = 12,102,503 (1.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 370,714,160 number of mapped paired reads (second in pair) = 370,378,850 number of mapped paired reads (both in pair) = 739,497,778 number of mapped paired reads (singletons) = 1,595,232 number of mapped bases = 106,875,707,441 bp number of sequenced bases = 106,845,951,787 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 328,092,554 duplication rate = 41.35% >>>>>>> Insert size mean insert size = 42,319.754 std insert size = 2,015,400.8294 median insert size = 236 >>>>>>> Mapping quality mean mapping quality = 55.1633 >>>>>>> ACTG content number of A's = 31,998,729,695 bp (29.95%) number of C's = 21,651,798,989 bp (20.26%) number of T's = 30,565,646,950 bp (28.61%) number of G's = 22,629,122,885 bp (21.18%) number of N's = 653,268 bp (0%) GC percentage = 41.44% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 545,349,918 number of insertions = 13,739,326 mapped reads with insertion percentage = 1.82% number of deletions = 12,154,074 mapped reads with deletion percentage = 1.61% homopolymer indels = 48.57% >>>>>>> Coverage mean coverageData = 34.524X std coverageData = 81.8748X There is a 91.33% of reference with a coverageData >= 1X There is a 90.73% of reference with a coverageData >= 2X There is a 90.02% of reference with a coverageData >= 3X There is a 89.23% of reference with a coverageData >= 4X There is a 88.31% of reference with a coverageData >= 5X There is a 87.29% of reference with a coverageData >= 6X There is a 86.15% of reference with a coverageData >= 7X There is a 84.9% of reference with a coverageData >= 8X There is a 83.55% of reference with a coverageData >= 9X There is a 82.1% of reference with a coverageData >= 10X There is a 80.57% of reference with a coverageData >= 11X There is a 78.97% of reference with a coverageData >= 12X There is a 77.3% of reference with a coverageData >= 13X There is a 75.58% of reference with a coverageData >= 14X There is a 73.81% of reference with a coverageData >= 15X There is a 72% of reference with a coverageData >= 16X There is a 70.17% of reference with a coverageData >= 17X There is a 68.31% of reference with a coverageData >= 18X There is a 66.45% of reference with a coverageData >= 19X There is a 64.58% of reference with a coverageData >= 20X There is a 62.71% of reference with a coverageData >= 21X There is a 60.85% of reference with a coverageData >= 22X There is a 59% of reference with a coverageData >= 23X There is a 57.17% of reference with a coverageData >= 24X There is a 55.37% of reference with a coverageData >= 25X There is a 53.59% of reference with a coverageData >= 26X There is a 51.84% of reference with a coverageData >= 27X There is a 50.12% of reference with a coverageData >= 28X There is a 48.44% of reference with a coverageData >= 29X There is a 46.79% of reference with a coverageData >= 30X There is a 45.19% of reference with a coverageData >= 31X There is a 43.62% of reference with a coverageData >= 32X There is a 42.09% of reference with a coverageData >= 33X There is a 40.61% of reference with a coverageData >= 34X There is a 39.16% of reference with a coverageData >= 35X There is a 37.76% of reference with a coverageData >= 36X There is a 36.41% of reference with a coverageData >= 37X There is a 35.09% of reference with a coverageData >= 38X There is a 33.81% of reference with a coverageData >= 39X There is a 32.58% of reference with a coverageData >= 40X There is a 31.39% of reference with a coverageData >= 41X There is a 30.24% of reference with a coverageData >= 42X There is a 29.12% of reference with a coverageData >= 43X There is a 28.05% of reference with a coverageData >= 44X There is a 27.01% of reference with a coverageData >= 45X There is a 26.01% of reference with a coverageData >= 46X There is a 25.05% of reference with a coverageData >= 47X There is a 24.12% of reference with a coverageData >= 48X There is a 23.23% of reference with a coverageData >= 49X There is a 22.37% of reference with a coverageData >= 50X There is a 21.54% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9202682876 36.92140400324218 36.611437667694375 chr2 243199373 9284003014 38.17445291686669 134.12163406304003 chr3 198022430 7588867052 38.32327000532212 30.083334794440717 chr4 191154276 6572084196 34.381047254208426 26.8658370664155 chr5 180915260 6474326993 35.78651680902982 28.349813134399398 chr6 171115067 6163493535 36.019584032305 30.345711862979094 chr7 159138663 5717108144 35.92532472137208 29.130010059271008 chr8 146364022 5348333170 36.54131047314346 29.049945791471675 chr9 141213431 4543092391 32.17181509455712 35.500112563061094 chr10 135534747 4991230493 36.826205851109165 40.54489486796843 chr11 135006516 5215555887 38.63188267890714 32.15180211403717 chr12 133851895 5223222531 39.022402566657725 31.80517483618858 chr13 115169878 3366991742 29.235003114269166 27.997753759634595 chr14 107349540 3411388812 31.778327247606278 33.19136921791325 chr15 102531392 3398289041 33.14388866387379 34.438618323364814 chr16 90354753 3073225493 34.01288134781355 56.95388352649912 chr17 81195210 3065299789 37.75222441077497 43.60019822077225 chr18 78077248 2860873557 36.641577799975735 32.87762566722289 chr19 59128983 1934413388 32.71514729079646 35.1992824349378 chr20 63025520 2597847128 41.21897174350961 36.304479929278614 chr21 48129895 1473506984 30.61521293574399 36.416080921912254 chr22 51304566 1540864303 30.033668016994824 38.57573063028354 chrMT 16571 435086962 26255.926739484643 10226.8328246169 chrX 155270560 2848995659 18.348588805244212 17.23523330747155 chrY 59373566 544924301 9.177894098528627 30.305554087798654