BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173899.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 10,056,336 number of mapped reads = 9,791,787 (97.37%) number of supplementary alignments = 1,014,495 (10.09%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,896,344 number of mapped paired reads (second in pair) = 4,895,443 number of mapped paired reads (both in pair) = 9,616,942 number of mapped paired reads (singletons) = 174,845 number of mapped bases = 1,158,127,519 bp number of sequenced bases = 1,157,436,079 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,829,893 duplication rate = 66.14% >>>>>>> Insert size mean insert size = 806,328.0422 std insert size = 7,971,417.303 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 52.5698 >>>>>>> ACTG content number of A's = 350,403,493 bp (30.27%) number of C's = 224,456,749 bp (19.39%) number of T's = 349,347,122 bp (30.18%) number of G's = 233,215,399 bp (20.15%) number of N's = 13,316 bp (0%) GC percentage = 39.54% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 11,757,885 number of insertions = 122,825 mapped reads with insertion percentage = 1.21% number of deletions = 287,632 mapped reads with deletion percentage = 2.87% homopolymer indels = 42.71% >>>>>>> Coverage mean coverageData = 0.3741X std coverageData = 5.4679X There is a 7.05% of reference with a coverageData >= 1X There is a 5.68% of reference with a coverageData >= 2X There is a 4.5% of reference with a coverageData >= 3X There is a 3.77% of reference with a coverageData >= 4X There is a 2.97% of reference with a coverageData >= 5X There is a 2.45% of reference with a coverageData >= 6X There is a 1.89% of reference with a coverageData >= 7X There is a 1.56% of reference with a coverageData >= 8X There is a 1.19% of reference with a coverageData >= 9X There is a 1% of reference with a coverageData >= 10X There is a 0.77% of reference with a coverageData >= 11X There is a 0.66% of reference with a coverageData >= 12X There is a 0.51% of reference with a coverageData >= 13X There is a 0.44% of reference with a coverageData >= 14X There is a 0.34% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.21% of reference with a coverageData >= 18X There is a 0.16% of reference with a coverageData >= 19X There is a 0.14% of reference with a coverageData >= 20X There is a 0.11% of reference with a coverageData >= 21X There is a 0.1% of reference with a coverageData >= 22X There is a 0.08% of reference with a coverageData >= 23X There is a 0.07% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 104010179 0.41729155411010993 2.938989432742846 chr2 243199373 85450275 0.35135894449859456 16.41350201947887 chr3 198022430 71036100 0.3587275441473978 1.8233941401841423 chr4 191154276 72297100 0.3782133547459854 2.6042279024223234 chr5 180915260 58104244 0.32116828619100457 1.6830553636735737 chr6 171115067 56715779 0.3314481886039877 1.8822837251178068 chr7 159138663 101198899 0.6359164837271506 5.834652936875092 chr8 146364022 116173856 0.7937323285636412 3.6622414387040676 chr9 141213431 41373176 0.29298329278608065 2.431792667324877 chr10 135534747 53285202 0.39314790619707285 7.350786221406599 chr11 135006516 47440459 0.3513938467977353 1.875222237948043 chr12 133851895 43726671 0.3266795064799045 1.745637829101193 chr13 115169878 29215814 0.25367582659069937 1.5212593419850564 chr14 107349540 39027789 0.3635580459869693 1.8493794083329116 chr15 102531392 28045154 0.27352748707439767 1.5642566576119241 chr16 90354753 26404544 0.29223193161736605 2.807705338628937 chr17 81195210 32400406 0.3990433179494209 2.253260655151387 chr18 78077248 20567609 0.2634264081643861 3.265991466437869 chr19 59128983 15279397 0.25840791139600694 2.252235234646118 chr20 63025520 42662274 0.6769047522336984 2.5796431943694613 chr21 48129895 13925337 0.28932822313449885 1.8145065062880523 chr22 51304566 11417410 0.22254179091973997 1.359518831527273 chrMT 16571 3236251 195.29605938084606 147.96776253609085 chrX 155270560 43075158 0.2774199951362319 1.609728676052833 chrY 59373566 2058436 0.034669233106194096 1.41954689866416