BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926979.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 32,902,716 number of mapped reads = 32,386,897 (98.43%) number of supplementary alignments = 423,401 (1.29%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,252,652 number of mapped paired reads (second in pair) = 16,134,245 number of mapped paired reads (both in pair) = 32,099,234 number of mapped paired reads (singletons) = 287,663 number of mapped bases = 3,042,701,992 bp number of sequenced bases = 3,040,407,090 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,783,189 duplication rate = 6.58% >>>>>>> Insert size mean insert size = 127,780.9593 std insert size = 3,474,529.676 median insert size = 179 >>>>>>> Mapping quality mean mapping quality = 53.5093 >>>>>>> ACTG content number of A's = 862,407,881 bp (28.36%) number of C's = 612,867,898 bp (20.16%) number of T's = 876,851,360 bp (28.84%) number of G's = 688,004,691 bp (22.63%) number of N's = 275,260 bp (0.01%) GC percentage = 42.79% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 28,135,700 number of insertions = 493,766 mapped reads with insertion percentage = 1.5% number of deletions = 1,604,754 mapped reads with deletion percentage = 4.83% homopolymer indels = 52.74% >>>>>>> Coverage mean coverageData = 0.9829X std coverageData = 3.8871X There is a 34.04% of reference with a coverageData >= 1X There is a 20.62% of reference with a coverageData >= 2X There is a 12.84% of reference with a coverageData >= 3X There is a 8.47% of reference with a coverageData >= 4X There is a 5.74% of reference with a coverageData >= 5X There is a 3.99% of reference with a coverageData >= 6X There is a 2.82% of reference with a coverageData >= 7X There is a 2.03% of reference with a coverageData >= 8X There is a 1.48% of reference with a coverageData >= 9X There is a 1.09% of reference with a coverageData >= 10X There is a 0.81% of reference with a coverageData >= 11X There is a 0.61% of reference with a coverageData >= 12X There is a 0.46% of reference with a coverageData >= 13X There is a 0.35% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.21% of reference with a coverageData >= 16X There is a 0.16% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.1% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% 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 0.01% 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 239742278 0.9618522795977307 4.278307905690583 chr2 243199373 266567005 1.0960842608751298 7.100409618944611 chr3 198022430 208928431 1.0550745741277894 2.1510419363317697 chr4 191154276 186307743 0.9746459608363666 3.6007329989804657 chr5 180915260 184534332 1.0200042384484316 2.097209422887197 chr6 171115067 175336493 1.0246701010846695 2.8209628833637197 chr7 159138663 158924170 0.998652162862522 2.90871554163688 chr8 146364022 156712438 1.0707032770662726 2.67282536213576 chr9 141213431 132299059 0.9368730584840758 4.6375290853114235 chr10 135534747 154153914 1.1373755985983431 6.033723113090659 chr11 135006516 146341598 1.0839595179243051 3.111589205180761 chr12 133851895 138847903 1.037324895549667 2.4134189244534783 chr13 115169878 87202879 0.7571674166399656 1.87746153361801 chr14 107349540 86939442 0.8098725155226562 1.940194265823648 chr15 102531392 88217307 0.8603931467154957 2.0598019658233957 chr16 90354753 96988826 1.0734225127038972 7.243843431810759 chr17 81195210 79085934 0.9740221621447867 3.02649685971773 chr18 78077248 80661370 1.033096991328383 5.012223980310429 chr19 59128983 46623891 0.7885116339646836 2.9582642162634207 chr20 63025520 71112758 1.1283168786231355 2.535393442650868 chr21 48129895 38112582 0.7918692114329358 2.901146084364884 chr22 51304566 39438146 0.7687063564673756 2.0421964185596155 chrMT 16571 134229 8.100235350914248 7.483078226836923 chrX 155270560 173904352 1.1200085322034004 2.5354098436782273 chrY 59373566 5584912 0.09406394758232982 3.2707354695016284