BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779303.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 = 17,741,818 number of mapped reads = 17,146,558 (96.64%) number of supplementary alignments = 41,899 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,627,392 number of mapped paired reads (second in pair) = 8,519,166 number of mapped paired reads (both in pair) = 17,011,242 number of mapped paired reads (singletons) = 135,316 number of mapped bases = 1,364,992,017 bp number of sequenced bases = 1,364,732,699 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 542,472 duplication rate = 2.92% >>>>>>> Insert size mean insert size = 38,898.0693 std insert size = 1,850,366.6093 median insert size = 223 >>>>>>> Mapping quality mean mapping quality = 52.9366 >>>>>>> ACTG content number of A's = 421,903,946 bp (30.91%) number of C's = 258,719,787 bp (18.96%) number of T's = 419,672,469 bp (30.75%) number of G's = 264,077,147 bp (19.35%) number of N's = 359,350 bp (0.03%) GC percentage = 38.31% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 5,053,116 number of insertions = 98,976 mapped reads with insertion percentage = 0.57% number of deletions = 126,320 mapped reads with deletion percentage = 0.73% homopolymer indels = 46.48% >>>>>>> Coverage mean coverageData = 0.4409X std coverageData = 1.6265X There is a 17.91% of reference with a coverageData >= 1X There is a 8.92% of reference with a coverageData >= 2X There is a 5.2% of reference with a coverageData >= 3X There is a 3.31% of reference with a coverageData >= 4X There is a 2.22% of reference with a coverageData >= 5X There is a 1.55% of reference with a coverageData >= 6X There is a 1.11% of reference with a coverageData >= 7X There is a 0.81% of reference with a coverageData >= 8X There is a 0.61% of reference with a coverageData >= 9X There is a 0.46% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.22% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.14% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% 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 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 92161755 0.3697553676305585 1.953407992667097 chr2 243199373 119040374 0.48947648397103394 1.5406156058551337 chr3 198022430 95270382 0.48110904406132177 1.5488508948449655 chr4 191154276 115608369 0.6047909124460287 1.716780166279516 chr5 180915260 94091655 0.5200868904038277 1.6519988976845688 chr6 171115067 99912821 0.5838925978388566 1.756183902106797 chr7 159138663 76706634 0.48201130105007856 1.727825069249391 chr8 146364022 86376695 0.5901497773817667 1.619614887026268 chr9 141213431 44006040 0.3116278649160504 1.1872541657839812 chr10 135534747 59191940 0.43672889284989036 2.8058906644928765 chr11 135006516 76196602 0.5643920327519599 1.6832326201936199 chr12 133851895 51680073 0.3860989267279331 1.3519376511692107 chr13 115169878 47812622 0.4151486728152998 1.393952478877474 chr14 107349540 46409919 0.43232527125873105 1.5591542379953645 chr15 102531392 22421555 0.21867990439454874 0.8941526153622517 chr16 90354753 21902571 0.24240640666684132 0.9025193371583284 chr17 81195210 15440399 0.19016391484177453 0.8768287816024757 chr18 78077248 39382977 0.50441041415804 1.4468856581185698 chr19 59128983 13182321 0.22294178474201054 1.454058413593859 chr20 63025520 15378293 0.24400104909884124 1.067541439288407 chr21 48129895 21022073 0.4367778695548785 1.4569849264662649 chr22 51304566 3609711 0.07035847452641934 0.446966090954055 chrMT 16571 1066 0.06432924989439381 0.3443926557673427 chrX 155270560 107299736 0.6910500999030338 1.9732017138705449 chrY 59373566 885434 0.014912932802452863 0.18669892843980904