BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617383.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,245,153 (94.52%) number of supplementary alignments = 96,378 (0.3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,225,657 number of mapped paired reads (second in pair) = 15,019,496 number of mapped paired reads (both in pair) = 29,694,086 number of mapped paired reads (singletons) = 551,067 number of mapped bases = 2,967,106,103 bp number of sequenced bases = 2,966,226,539 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,613,898 duplication rate = 1.52% >>>>>>> Insert size mean insert size = 66,361.3299 std insert size = 2,474,716.8704 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 53.4193 >>>>>>> ACTG content number of A's = 898,968,904 bp (30.31%) number of C's = 588,370,277 bp (19.84%) number of T's = 887,712,236 bp (29.93%) number of G's = 590,369,491 bp (19.9%) number of N's = 805,631 bp (0.03%) GC percentage = 39.74% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 28,786,307 number of insertions = 301,623 mapped reads with insertion percentage = 0.97% number of deletions = 363,011 mapped reads with deletion percentage = 1.16% homopolymer indels = 41.28% >>>>>>> Coverage mean coverageData = 0.9585X std coverageData = 9.8688X There is a 53.06% of reference with a coverageData >= 1X There is a 23.97% of reference with a coverageData >= 2X There is a 9.21% of reference with a coverageData >= 3X There is a 3.23% of reference with a coverageData >= 4X There is a 1.11% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% 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 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 192869645 0.773798052041764 20.094704751177588 chr2 243199373 293032332 1.2049057873187856 8.944199058079898 chr3 198022430 236127733 1.1924292263255227 1.4881807020204203 chr4 191154276 162581564 0.85052538400972 9.438359433934975 chr5 180915260 186111176 1.0287201643465564 1.4613230007605638 chr6 171115067 139053317 0.8126304681282099 3.655276630210759 chr7 159138663 240639224 1.5121355141710597 10.892894322371626 chr8 146364022 125005834 0.8540748764064436 7.661007320621596 chr9 141213431 125104506 0.885924979756352 15.117611638705762 chr10 135534747 124917084 0.9216609523755558 20.24504195230227 chr11 135006516 158997604 1.1777031858225273 5.617487344619221 chr12 133851895 130954337 0.9783525067015301 1.3923243286718934 chr13 115169878 129098116 1.1209364656963516 1.3415708661265655 chr14 107349540 85941752 0.8005786703883407 1.3759878208541518 chr15 102531392 66643412 0.6499805640013158 1.125211337704964 chr16 90354753 74657657 0.8262726035010023 7.9346360720891305 chr17 81195210 92419983 1.1382442757399112 7.205124547174982 chr18 78077248 53807192 0.6891532857305627 15.417236549814813 chr19 59128983 54985487 0.9299244500789063 9.532403181328823 chr20 63025520 84876387 1.3466987182335028 2.4782099790743484 chr21 48129895 47244646 0.981607086406484 3.228990544285425 chr22 51304566 26445900 0.5154687401507304 0.9356519353703415 chrMT 16571 2018861 121.83096976645948 20.261100560232208 chrX 155270560 123361379 0.7944930384742607 3.052557772397876 chrY 59373566 10210975 0.1719784693410532 8.4651585246955