BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779405.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 = 22,632,936 number of mapped reads = 20,281,028 (89.61%) number of supplementary alignments = 428,928 (1.9%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,200,932 number of mapped paired reads (second in pair) = 10,080,096 number of mapped paired reads (both in pair) = 20,090,006 number of mapped paired reads (singletons) = 191,022 number of mapped bases = 1,603,659,535 bp number of sequenced bases = 1,603,500,414 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,076,780 duplication rate = 28.94% >>>>>>> Insert size mean insert size = 105,494.366 std insert size = 3,440,203.7624 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 49.504 >>>>>>> ACTG content number of A's = 480,461,525 bp (29.96%) number of C's = 319,681,620 bp (19.94%) number of T's = 475,265,338 bp (29.64%) number of G's = 327,739,411 bp (20.44%) number of N's = 352,520 bp (0.02%) GC percentage = 40.38% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 5,541,237 number of insertions = 87,077 mapped reads with insertion percentage = 0.43% number of deletions = 89,489 mapped reads with deletion percentage = 0.44% homopolymer indels = 48.28% >>>>>>> Coverage mean coverageData = 0.518X std coverageData = 227.8537X There is a 1.82% of reference with a coverageData >= 1X There is a 0.86% of reference with a coverageData >= 2X There is a 0.58% of reference with a coverageData >= 3X There is a 0.46% of reference with a coverageData >= 4X There is a 0.38% of reference with a coverageData >= 5X There is a 0.33% of reference with a coverageData >= 6X There is a 0.29% of reference with a coverageData >= 7X There is a 0.26% of reference with a coverageData >= 8X There is a 0.24% of reference with a coverageData >= 9X There is a 0.22% of reference with a coverageData >= 10X There is a 0.2% of reference with a coverageData >= 11X There is a 0.19% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.13% of reference with a coverageData >= 19X There is a 0.12% of reference with a coverageData >= 20X There is a 0.12% 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 0.11% of reference with a coverageData >= 24X There is a 0.1% of reference with a coverageData >= 25X There is a 0.1% of reference with a coverageData >= 26X There is a 0.1% of reference with a coverageData >= 27X There is a 0.09% of reference with a coverageData >= 28X There is a 0.09% of reference with a coverageData >= 29X There is a 0.09% of reference with a coverageData >= 30X There is a 0.09% of reference with a coverageData >= 31X There is a 0.08% of reference with a coverageData >= 32X There is a 0.08% of reference with a coverageData >= 33X There is a 0.08% of reference with a coverageData >= 34X There is a 0.08% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.07% of reference with a coverageData >= 38X There is a 0.07% of reference with a coverageData >= 39X There is a 0.07% of reference with a coverageData >= 40X There is a 0.07% of reference with a coverageData >= 41X There is a 0.07% of reference with a coverageData >= 42X There is a 0.07% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.06% of reference with a coverageData >= 46X There is a 0.06% of reference with a coverageData >= 47X There is a 0.06% of reference with a coverageData >= 48X There is a 0.06% of reference with a coverageData >= 49X There is a 0.06% of reference with a coverageData >= 50X There is a 0.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 191693385 0.7690788662067165 246.29785848944863 chr2 243199373 161541351 0.664234241261798 271.748132118886 chr3 198022430 470952447 2.378278294029621 723.370158086617 chr4 191154276 143761701 0.7520715937319655 124.75042037463962 chr5 180915260 63503101 0.3510101967075635 21.91198908046432 chr6 171115067 26899078 0.15719876964428856 5.873842122809609 chr7 159138663 113475564 0.7130609360466978 91.31841266525733 chr8 146364022 26334360 0.17992372469786325 63.30694845239813 chr9 141213431 42292863 0.2994960373139011 17.10561312658937 chr10 135534747 23992692 0.17702244281313337 53.76678107025269 chr11 135006516 36357964 0.26930525338495515 24.45947681734668 chr12 133851895 70918198 0.529825879566367 104.8849916298412 chr13 115169878 19387901 0.16834176901706885 5.876723992024534 chr14 107349540 8926811 0.08315649047028986 5.605322916035426 chr15 102531392 122340516 1.193200576073326 406.45107601526604 chr16 90354753 5264377 0.05826342085180621 2.22430076885028 chr17 81195210 10094647 0.12432564679615953 22.690264263614925 chr18 78077248 11796695 0.151090046104084 9.539566674444776 chr19 59128983 21019735 0.3554895405523887 28.869522974643203 chr20 63025520 5710287 0.09060277487595501 4.276695799203683 chr21 48129895 17503000 0.3636617117074533 12.396149655353758 chr22 51304566 1465270 0.028560226004055857 1.263323164929438 chrMT 16571 346906 20.9345241687285 10.461547698962816 chrX 155270560 6806785 0.043838220200918966 1.8610291015191207 chrY 59373566 1273901 0.021455692925703672 0.5374407661166393