BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779084.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 = 11,288,790 number of mapped reads = 10,877,151 (96.35%) number of supplementary alignments = 59,551 (0.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,499,010 number of mapped paired reads (second in pair) = 5,378,141 number of mapped paired reads (both in pair) = 10,710,830 number of mapped paired reads (singletons) = 166,321 number of mapped bases = 1,085,225,469 bp number of sequenced bases = 1,084,981,299 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 286,426 duplication rate = 2.3% >>>>>>> Insert size mean insert size = 65,574.0966 std insert size = 2,422,190.6176 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 53.4616 >>>>>>> ACTG content number of A's = 330,052,492 bp (30.42%) number of C's = 211,446,191 bp (19.49%) number of T's = 328,499,325 bp (30.28%) number of G's = 214,617,788 bp (19.78%) number of N's = 365,503 bp (0.03%) GC percentage = 39.27% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 4,967,481 number of insertions = 89,229 mapped reads with insertion percentage = 0.81% number of deletions = 109,817 mapped reads with deletion percentage = 0.99% homopolymer indels = 46.36% >>>>>>> Coverage mean coverageData = 0.3506X std coverageData = 1.2571X There is a 19.72% of reference with a coverageData >= 1X There is a 8.1% of reference with a coverageData >= 2X There is a 3.3% of reference with a coverageData >= 3X There is a 1.51% of reference with a coverageData >= 4X There is a 0.74% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.22% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.09% 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 0.03% of reference with a coverageData >= 13X There is a 0.03% 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 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% 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 0.01% 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 0.01% 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% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 84376170 0.33851939730974634 1.6334962685538348 chr2 243199373 75875015 0.3119868857556635 0.9165999836633171 chr3 198022430 83195818 0.42013330510084135 0.9323086972355542 chr4 191154276 83038980 0.43440817405518045 0.9809060311852011 chr5 180915260 48072192 0.2657166233517283 0.7548886086184906 chr6 171115067 50597901 0.29569518270416245 0.8280808365640894 chr7 159138663 111886146 0.7030733065791812 3.33341381766038 chr8 146364022 91168423 0.6228882054088402 1.2077121013250294 chr9 141213431 46346657 0.3282028959412508 0.9354022485465086 chr10 135534747 23299986 0.171911532029495 1.547964301351745 chr11 135006516 53429290 0.39575341682026666 0.9628711189457254 chr12 133851895 39372416 0.294149111598308 0.8232900856228405 chr13 115169878 17884288 0.15528615911184693 0.5924392733477789 chr14 107349540 39026466 0.3635457217608944 0.9281588330837072 chr15 102531392 20574474 0.20066511922514424 0.6837558681714239 chr16 90354753 23334982 0.2582595959285064 0.7401039722171535 chr17 81195210 18888430 0.23262985587450294 0.7321556901751728 chr18 78077248 23635839 0.3027237717190032 0.8365773825967321 chr19 59128983 15140092 0.25605196016985443 1.1562268320599376 chr20 63025520 27044733 0.4291076535346317 0.9646403095219971 chr21 48129895 14303477 0.2971848785458601 0.8047392888700098 chr22 51304566 5866514 0.11434682051496158 0.5743952343950693 chrMT 16571 639 0.038561342103675095 0.2560426922637062 chrX 155270560 88100972 0.5674029384578764 1.1802898834171491 chrY 59373566 765569 0.012894105097207738 0.2036624168599495