BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038462.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 18,644,106 number of mapped reads = 17,149,743 (91.98%) number of supplementary alignments = 251,503 (1.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,696,718 number of mapped paired reads (second in pair) = 8,453,025 number of mapped paired reads (both in pair) = 16,849,168 number of mapped paired reads (singletons) = 300,575 number of mapped bases = 2,311,097,299 bp number of sequenced bases = 2,309,488,936 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,490,111 duplication rate = 14.53% >>>>>>> Insert size mean insert size = 81,852.0833 std insert size = 2,781,182.0232 median insert size = 255 >>>>>>> Mapping quality mean mapping quality = 53.467 >>>>>>> ACTG content number of A's = 658,760,144 bp (28.52%) number of C's = 460,595,055 bp (19.94%) number of T's = 669,131,685 bp (28.97%) number of G's = 520,817,839 bp (22.55%) number of N's = 184,213 bp (0.01%) GC percentage = 42.49% >>>>>>> Mismatches and indels general error rate = 0.013 number of mismatches = 28,936,861 number of insertions = 404,167 mapped reads with insertion percentage = 2.24% number of deletions = 844,503 mapped reads with deletion percentage = 4.75% homopolymer indels = 47.96% >>>>>>> Coverage mean coverageData = 0.7466X std coverageData = 9.3029X There is a 27.05% of reference with a coverageData >= 1X There is a 16.05% of reference with a coverageData >= 2X There is a 9.49% of reference with a coverageData >= 3X There is a 6.05% of reference with a coverageData >= 4X There is a 3.86% of reference with a coverageData >= 5X There is a 2.54% of reference with a coverageData >= 6X There is a 1.7% of reference with a coverageData >= 7X There is a 1.16% of reference with a coverageData >= 8X There is a 0.8% of reference with a coverageData >= 9X There is a 0.56% of reference with a coverageData >= 10X There is a 0.4% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.22% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% 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 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% 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 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 200897316 0.8060052777160382 13.419196413985192 chr2 243199373 207526254 0.8533173891036306 10.443472221956284 chr3 198022430 168092481 0.8488557634607352 1.8924824548625043 chr4 191154276 98514116 0.5153644378847168 9.640576506444992 chr5 180915260 159407708 0.8811180881037896 1.8718968839160581 chr6 171115067 133996696 0.783079470143912 7.683956571655786 chr7 159138663 110775159 0.6960920552662931 9.232741303341834 chr8 146364022 146703772 1.002321267175891 3.8504843729881295 chr9 141213431 98084572 0.6945838742491852 16.1261945608403 chr10 135534747 139623533 1.0301678063412034 22.28264054234687 chr11 135006516 103764746 0.7685906508394009 7.523274852118986 chr12 133851895 94944259 0.7093232337129034 1.8269517394020889 chr13 115169878 77450702 0.6724909615689616 1.5834965741341098 chr14 107349540 75451868 0.7028615865517449 1.7233153399506678 chr15 102531392 63504629 0.6193676664411227 1.56700948112995 chr16 90354753 70020688 0.7749530121564274 8.270696384471064 chr17 81195210 57511542 0.7083120051047346 11.942033027205637 chr18 78077248 93214706 1.1938779655758358 10.994474781855713 chr19 59128983 30444728 0.5148867180752965 5.826769014218342 chr20 63025520 62038554 0.9843402164710422 3.562059746598213 chr21 48129895 22673548 0.4710907430818206 4.7805220617624355 chr22 51304566 13240691 0.2580801677573883 0.9868516694137094 chrMT 16571 3016308 182.0232937058717 107.86905604445029 chrX 155270560 75625054 0.48705339891863597 2.11904271193318 chrY 59373566 4573669 0.07703207518308737 9.95239047512259