BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779289.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 = 22,855,742 number of mapped reads = 22,173,413 (97.01%) number of supplementary alignments = 50,298 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,200,295 number of mapped paired reads (second in pair) = 10,973,118 number of mapped paired reads (both in pair) = 21,917,244 number of mapped paired reads (singletons) = 256,169 number of mapped bases = 1,765,047,102 bp number of sequenced bases = 1,764,727,787 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 450,130 duplication rate = 1.87% >>>>>>> Insert size mean insert size = 42,378.2071 std insert size = 1,948,454.2918 median insert size = 205 >>>>>>> Mapping quality mean mapping quality = 52.9747 >>>>>>> ACTG content number of A's = 538,876,609 bp (30.54%) number of C's = 341,129,957 bp (19.33%) number of T's = 538,113,115 bp (30.49%) number of G's = 346,277,183 bp (19.62%) number of N's = 330,923 bp (0.02%) GC percentage = 38.95% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 6,705,894 number of insertions = 124,839 mapped reads with insertion percentage = 0.56% number of deletions = 154,409 mapped reads with deletion percentage = 0.69% homopolymer indels = 46.59% >>>>>>> Coverage mean coverageData = 0.5702X std coverageData = 1.4307X There is a 29.13% of reference with a coverageData >= 1X There is a 12.92% of reference with a coverageData >= 2X There is a 6.27% of reference with a coverageData >= 3X There is a 3.28% of reference with a coverageData >= 4X There is a 1.82% of reference with a coverageData >= 5X There is a 1.06% of reference with a coverageData >= 6X There is a 0.65% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.27% of reference with a coverageData >= 9X There is a 0.19% of reference with a coverageData >= 10X There is a 0.13% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% 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 0.01% of reference with a coverageData >= 26X There is a 0.01% 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% 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 137930344 0.5533801418292154 1.397987152424982 chr2 243199373 154240719 0.6342151178161137 1.2420814508918432 chr3 198022430 128281074 0.6478108262786191 1.2986082347507848 chr4 191154276 138626426 0.7252070364358473 1.3885049822277413 chr5 180915260 98848421 0.5463796752136885 1.1594764199618435 chr6 171115067 105743968 0.617969941828676 1.24856212704677 chr7 159138663 150606644 0.9463862593843709 3.2050817326385266 chr8 146364022 145164255 0.9918028557591838 1.6569853957492542 chr9 141213431 64795634 0.4588489461742488 1.1236559350648738 chr10 135534747 30541575 0.2253412920009361 1.5136644443961502 chr11 135006516 76697037 0.5680987797655633 1.2041579855727496 chr12 133851895 83452785 0.6234710759978408 1.2683225642600557 chr13 115169878 52358144 0.4546166489817763 1.0440603030540023 chr14 107349540 56058085 0.5222014458562189 1.1801928204161394 chr15 102531392 29933134 0.2919411647117792 0.8455727259437957 chr16 90354753 22622601 0.25037532889941055 0.7210787568501077 chr17 81195210 30221392 0.37220658706344867 0.9454557500658547 chr18 78077248 49898692 0.6390938881452379 1.2464095097853571 chr19 59128983 17364789 0.293676436139617 0.9166187057748064 chr20 63025520 39952074 0.6339031236870398 1.3217247578958016 chr21 48129895 19978553 0.41509654238805216 0.9910830157617851 chr22 51304566 10806572 0.21063567714421363 0.6928831753793773 chrMT 16571 889 0.053647939170840625 0.32098256967353195 chrX 155270560 119617503 0.7703810883402494 1.5382948915337282 chrY 59373566 1305792 0.021992817477057044 0.2524093186536579