BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779306.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 18,691,128 number of mapped reads = 16,933,997 (90.6%) number of supplementary alignments = 53,131 (0.28%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,525,219 number of mapped paired reads (second in pair) = 8,408,778 number of mapped paired reads (both in pair) = 16,773,474 number of mapped paired reads (singletons) = 160,523 number of mapped bases = 1,347,178,966 bp number of sequenced bases = 1,346,910,593 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 852,815 duplication rate = 4.58% >>>>>>> Insert size mean insert size = 48,721.868 std insert size = 2,035,560.4362 median insert size = 209 >>>>>>> Mapping quality mean mapping quality = 52.807 >>>>>>> ACTG content number of A's = 417,165,474 bp (30.97%) number of C's = 255,142,826 bp (18.94%) number of T's = 413,257,015 bp (30.68%) number of G's = 260,988,454 bp (19.38%) number of N's = 356,824 bp (0.03%) GC percentage = 38.32% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 4,833,172 number of insertions = 100,739 mapped reads with insertion percentage = 0.59% number of deletions = 130,892 mapped reads with deletion percentage = 0.76% homopolymer indels = 46.46% >>>>>>> Coverage mean coverageData = 0.4352X std coverageData = 1.9981X There is a 15.58% of reference with a coverageData >= 1X There is a 7.43% of reference with a coverageData >= 2X There is a 4.5% of reference with a coverageData >= 3X There is a 3.08% of reference with a coverageData >= 4X There is a 2.26% of reference with a coverageData >= 5X There is a 1.72% of reference with a coverageData >= 6X There is a 1.35% of reference with a coverageData >= 7X There is a 1.08% of reference with a coverageData >= 8X There is a 0.88% of reference with a coverageData >= 9X There is a 0.72% of reference with a coverageData >= 10X There is a 0.6% of reference with a coverageData >= 11X There is a 0.51% of reference with a coverageData >= 12X There is a 0.43% of reference with a coverageData >= 13X There is a 0.37% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.21% of reference with a coverageData >= 18X There is a 0.18% of reference with a coverageData >= 19X There is a 0.16% of reference with a coverageData >= 20X There is a 0.14% of reference with a coverageData >= 21X There is a 0.12% of reference with a coverageData >= 22X There is a 0.11% of reference with a coverageData >= 23X There is a 0.1% 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 0.06% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.05% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% 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 90598688 0.3634843020110269 2.28566365150891 chr2 243199373 111416744 0.45812924032497404 1.8215825943380681 chr3 198022430 75535449 0.38144895505019305 1.7872712746929762 chr4 191154276 96603681 0.5053702329944217 2.0586454266981167 chr5 180915260 101917591 0.5633443580160126 2.14279500940006 chr6 171115067 60515019 0.35365102594969033 1.4729177776979696 chr7 159138663 127081115 0.7985558795350693 3.0388253595080545 chr8 146364022 118805904 0.8117152178286 2.6280945855162647 chr9 141213431 58553286 0.41464388752086906 1.8201829106627154 chr10 135534747 19295960 0.14236910037541886 1.558915993308464 chr11 135006516 81695148 0.6051200373173099 2.26579949134549 chr12 133851895 57581301 0.4301866701252156 1.6977186753585163 chr13 115169878 28349761 0.2461560391685055 1.0570194716300685 chr14 107349540 41277770 0.3845174371497074 1.6256182854466044 chr15 102531392 32899535 0.3208728015708594 1.756775719278891 chr16 90354753 17183481 0.19017794227161464 0.8995938516695406 chr17 81195210 13604477 0.16755270415582396 0.8792442725199872 chr18 78077248 31324048 0.4011930338528325 1.5569205387271037 chr19 59128983 13336181 0.22554389274714906 1.325915777594671 chr20 63025520 36778929 0.5835561372599544 2.1206604780818843 chr21 48129895 19834578 0.4121051583428553 2.1264870202971 chr22 51304566 6390044 0.12455117542559467 0.9328365640801346 chrMT 16571 1515 0.0914247782270231 0.3107001239900025 chrX 155270560 105669873 0.680553177627491 3.037496196493695 chrY 59373566 928888 0.015644807320483328 0.21375728011166512