BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124835.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 603,465,272 number of mapped reads = 598,645,038 (99.2%) number of supplementary alignments = 5,420,843 (0.9%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 300,366,112 number of mapped paired reads (second in pair) = 298,278,926 number of mapped paired reads (both in pair) = 595,851,052 number of mapped paired reads (singletons) = 2,793,986 number of mapped bases = 87,896,729,888 bp number of sequenced bases = 87,860,546,887 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 139,647,062 duplication rate = 17.72% >>>>>>> Insert size mean insert size = 51,283.7937 std insert size = 2,162,758.0287 median insert size = 319 >>>>>>> Mapping quality mean mapping quality = 54.2807 >>>>>>> ACTG content number of A's = 25,852,512,940 bp (29.42%) number of C's = 18,081,122,433 bp (20.58%) number of T's = 25,821,157,079 bp (29.39%) number of G's = 18,103,424,432 bp (20.6%) number of N's = 2,330,003 bp (0%) GC percentage = 41.18% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 705,092,914 number of insertions = 10,853,372 mapped reads with insertion percentage = 1.69% number of deletions = 11,617,973 mapped reads with deletion percentage = 1.83% homopolymer indels = 40.54% >>>>>>> Coverage mean coverageData = 28.3932X std coverageData = 400.3034X There is a 92.32% of reference with a coverageData >= 1X There is a 92.26% of reference with a coverageData >= 2X There is a 92.19% of reference with a coverageData >= 3X There is a 92.12% of reference with a coverageData >= 4X There is a 92.02% of reference with a coverageData >= 5X There is a 91.89% of reference with a coverageData >= 6X There is a 91.71% of reference with a coverageData >= 7X There is a 91.48% of reference with a coverageData >= 8X There is a 91.17% of reference with a coverageData >= 9X There is a 90.77% of reference with a coverageData >= 10X There is a 90.26% of reference with a coverageData >= 11X There is a 89.64% of reference with a coverageData >= 12X There is a 88.9% of reference with a coverageData >= 13X There is a 88.02% of reference with a coverageData >= 14X There is a 87% of reference with a coverageData >= 15X There is a 85.83% of reference with a coverageData >= 16X There is a 84.47% of reference with a coverageData >= 17X There is a 82.92% of reference with a coverageData >= 18X There is a 81.13% of reference with a coverageData >= 19X There is a 79.09% of reference with a coverageData >= 20X There is a 76.75% of reference with a coverageData >= 21X There is a 74.11% of reference with a coverageData >= 22X There is a 71.15% of reference with a coverageData >= 23X There is a 67.87% of reference with a coverageData >= 24X There is a 64.28% of reference with a coverageData >= 25X There is a 60.42% of reference with a coverageData >= 26X There is a 56.33% of reference with a coverageData >= 27X There is a 52.06% of reference with a coverageData >= 28X There is a 47.69% of reference with a coverageData >= 29X There is a 43.29% of reference with a coverageData >= 30X There is a 38.93% of reference with a coverageData >= 31X There is a 34.68% of reference with a coverageData >= 32X There is a 30.6% of reference with a coverageData >= 33X There is a 26.75% of reference with a coverageData >= 34X There is a 23.17% of reference with a coverageData >= 35X There is a 19.89% of reference with a coverageData >= 36X There is a 16.93% of reference with a coverageData >= 37X There is a 14.29% of reference with a coverageData >= 38X There is a 11.97% of reference with a coverageData >= 39X There is a 9.96% of reference with a coverageData >= 40X There is a 8.24% of reference with a coverageData >= 41X There is a 6.78% of reference with a coverageData >= 42X There is a 5.56% of reference with a coverageData >= 43X There is a 4.55% of reference with a coverageData >= 44X There is a 3.72% of reference with a coverageData >= 45X There is a 3.05% of reference with a coverageData >= 46X There is a 2.51% of reference with a coverageData >= 47X There is a 2.08% of reference with a coverageData >= 48X There is a 1.73% of reference with a coverageData >= 49X There is a 1.46% of reference with a coverageData >= 50X There is a 1.25% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7243166929 29.05977485608752 997.2243060509898 chr2 243199373 7688240768 31.61291360730605 198.4887618268933 chr3 198022430 5879965600 29.69343220361451 21.152898186341744 chr4 191154276 6058969879 31.696753040460365 336.7464337667346 chr5 180915260 5376410663 29.717839517794133 25.70505576541313 chr6 171115067 5111778378 29.87333884514097 112.25715234753726 chr7 159138663 4789969369 30.09934404815252 221.28990278845967 chr8 146364022 4482379773 30.624874280921304 379.1522277459315 chr9 141213431 3827566989 27.104836713442648 509.929588059996 chr10 135534747 4816130777 35.53428831796174 848.9816923564044 chr11 135006516 4038051331 29.91004768243927 160.156121810065 chr12 133851895 3898580934 29.126079492561537 94.71165982390524 chr13 115169878 2849401580 24.740857848264802 14.93458778843481 chr14 107349540 2647389005 24.66139123651578 20.439946250178597 chr15 102531392 2487549489 24.26134514003282 53.57119991337334 chr16 90354753 2657835574 29.415559068597087 160.78454166139102 chr17 81195210 2370617053 29.196513599755452 205.52084134258007 chr18 78077248 2548583776 32.641823851168525 486.55726366604426 chr19 59128983 1664151385 28.14442766587073 436.05176934809407 chr20 63025520 1815745937 28.80969386686536 103.79891730223297 chr21 48129895 1245326842 25.87428960732202 169.31312613436958 chr22 51304566 1032372705 20.122433254771124 71.73880384174262 chrMT 16571 32270610 1947.4147607265704 187.23010854462467 chrX 155270560 2396348509 15.433373261486272 54.18802216765045 chrY 59373566 937926033 15.797030500071362 364.9472993749625