BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173915.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 = 14,866,146 number of mapped reads = 14,455,113 (97.24%) number of supplementary alignments = 1,395,926 (9.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,242,817 number of mapped paired reads (second in pair) = 7,212,296 number of mapped paired reads (both in pair) = 14,186,616 number of mapped paired reads (singletons) = 268,497 number of mapped bases = 1,709,199,932 bp number of sequenced bases = 1,708,246,119 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,416,753 duplication rate = 65.89% >>>>>>> Insert size mean insert size = 804,241.2711 std insert size = 8,079,160.7429 median insert size = 206 >>>>>>> Mapping quality mean mapping quality = 52.7088 >>>>>>> ACTG content number of A's = 514,331,314 bp (30.11%) number of C's = 334,897,133 bp (19.6%) number of T's = 512,796,378 bp (30.02%) number of G's = 346,201,146 bp (20.27%) number of N's = 20,148 bp (0%) GC percentage = 39.87% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 17,940,821 number of insertions = 179,600 mapped reads with insertion percentage = 1.2% number of deletions = 378,813 mapped reads with deletion percentage = 2.55% homopolymer indels = 43.33% >>>>>>> Coverage mean coverageData = 0.5521X std coverageData = 7.7234X There is a 10.3% of reference with a coverageData >= 1X There is a 8.36% of reference with a coverageData >= 2X There is a 6.67% of reference with a coverageData >= 3X There is a 5.59% of reference with a coverageData >= 4X There is a 4.39% of reference with a coverageData >= 5X There is a 3.61% of reference with a coverageData >= 6X There is a 2.78% of reference with a coverageData >= 7X There is a 2.29% of reference with a coverageData >= 8X There is a 1.75% of reference with a coverageData >= 9X There is a 1.47% of reference with a coverageData >= 10X There is a 1.13% of reference with a coverageData >= 11X There is a 0.97% of reference with a coverageData >= 12X There is a 0.75% of reference with a coverageData >= 13X There is a 0.65% of reference with a coverageData >= 14X There is a 0.5% of reference with a coverageData >= 15X There is a 0.44% of reference with a coverageData >= 16X There is a 0.34% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.21% of reference with a coverageData >= 20X There is a 0.17% of reference with a coverageData >= 21X There is a 0.15% of reference with a coverageData >= 22X There is a 0.12% of reference with a coverageData >= 23X There is a 0.11% of reference with a coverageData >= 24X There is a 0.09% of reference with a coverageData >= 25X There is a 0.08% of reference with a coverageData >= 26X There is a 0.07% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% 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 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 155516207 0.6239350833954391 3.973673912800699 chr2 243199373 126987305 0.5221530937088394 23.343041580987858 chr3 198022430 103403375 0.5221801136366219 2.16284288150594 chr4 191154276 103477129 0.541327827790784 3.544247331729186 chr5 180915260 85236220 0.47113891885073705 2.014094537075803 chr6 171115067 84732873 0.49518066693682794 2.3183738740901862 chr7 159138663 153496142 0.9645433680688897 9.010516879404781 chr8 146364022 164107424 1.121227893013216 5.243746463337671 chr9 141213431 61147293 0.43301329460651655 3.3287255947002077 chr10 135534747 80037402 0.59053050063981 10.323177348945558 chr11 135006516 70347325 0.5210661461703078 2.3155861400420163 chr12 133851895 64862126 0.48458130533004407 2.120930691183919 chr13 115169878 42608977 0.3699663292167419 1.7905111720083153 chr14 107349540 57071855 0.5316450820376128 2.2072529254119764 chr15 102531392 42141804 0.41101367276862877 1.910549605110689 chr16 90354753 40493311 0.44815916878218903 3.766717587773579 chr17 81195210 42804344 0.5271781919155083 2.7671235250153816 chr18 78077248 29849203 0.38230347206909754 4.8424096856966425 chr19 59128983 22690765 0.38375030059285814 3.1368578809519074 chr20 63025520 66073387 1.0483592519347718 3.256186726465501 chr21 48129895 21335562 0.4432912641924525 2.4681088568945864 chr22 51304566 18383591 0.3583227075734351 1.7516146304655913 chrMT 16571 3608430 217.75571782028845 149.4494940802495 chrX 155270560 65423912 0.42135426058874265 1.9974645331487484 chrY 59373566 3363970 0.056657705215145744 2.4120489557376326