BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779163.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 = 32,352,896 number of mapped reads = 31,067,869 (96.03%) number of supplementary alignments = 183,940 (0.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,657,032 number of mapped paired reads (second in pair) = 15,410,837 number of mapped paired reads (both in pair) = 30,692,678 number of mapped paired reads (singletons) = 375,191 number of mapped bases = 3,102,850,696 bp number of sequenced bases = 3,102,135,996 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,557,527 duplication rate = 4.51% >>>>>>> Insert size mean insert size = 64,464.7294 std insert size = 2,429,150.0292 median insert size = 219 >>>>>>> Mapping quality mean mapping quality = 53.1454 >>>>>>> ACTG content number of A's = 955,532,956 bp (30.8%) number of C's = 592,146,776 bp (19.09%) number of T's = 952,918,290 bp (30.72%) number of G's = 600,287,907 bp (19.35%) number of N's = 1,250,067 bp (0.04%) GC percentage = 38.44% >>>>>>> Mismatches and indels general error rate = 0.0044 number of mismatches = 13,084,834 number of insertions = 258,652 mapped reads with insertion percentage = 0.82% number of deletions = 319,440 mapped reads with deletion percentage = 1.01% homopolymer indels = 46.54% >>>>>>> Coverage mean coverageData = 1.0023X std coverageData = 3.1367X There is a 28.82% of reference with a coverageData >= 1X There is a 17.74% of reference with a coverageData >= 2X There is a 11.87% of reference with a coverageData >= 3X There is a 8.47% of reference with a coverageData >= 4X There is a 6.28% of reference with a coverageData >= 5X There is a 4.78% of reference with a coverageData >= 6X There is a 3.72% of reference with a coverageData >= 7X There is a 2.94% of reference with a coverageData >= 8X There is a 2.36% of reference with a coverageData >= 9X There is a 1.91% of reference with a coverageData >= 10X There is a 1.57% of reference with a coverageData >= 11X There is a 1.29% of reference with a coverageData >= 12X There is a 1.08% of reference with a coverageData >= 13X There is a 0.9% of reference with a coverageData >= 14X There is a 0.76% of reference with a coverageData >= 15X There is a 0.65% of reference with a coverageData >= 16X There is a 0.55% of reference with a coverageData >= 17X There is a 0.47% of reference with a coverageData >= 18X There is a 0.41% of reference with a coverageData >= 19X There is a 0.35% of reference with a coverageData >= 20X There is a 0.31% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.18% of reference with a coverageData >= 25X There is a 0.16% of reference with a coverageData >= 26X There is a 0.14% of reference with a coverageData >= 27X There is a 0.13% of reference with a coverageData >= 28X There is a 0.12% of reference with a coverageData >= 29X There is a 0.1% 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 0.07% of reference with a coverageData >= 34X There is a 0.06% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 260450965 1.0449360725965855 3.8976199578586286 chr2 243199373 245408267 1.0090826467714618 2.9500020894362966 chr3 198022430 220574630 1.1138870985473717 2.816355999586514 chr4 191154276 266229462 1.3927465687453415 3.036861730414698 chr5 180915260 182357417 1.0079714502800925 2.5850674042018427 chr6 171115067 207797856 1.2143749796153251 3.082781233892018 chr7 159138663 260183926 1.6349510615154534 5.1794168916918295 chr8 146364022 235549407 1.609339534274345 3.4763772682319516 chr9 141213431 107838642 0.763657119838693 2.421669683017016 chr10 135534747 71538335 0.5278228394081114 4.414374687958273 chr11 135006516 118611848 0.8785638761317268 2.5054485283418235 chr12 133851895 122574339 0.9157460116646089 2.724024491327287 chr13 115169878 117459012 1.019876151991756 2.6740058807690326 chr14 107349540 96435046 0.8983275196148954 2.56993025395228 chr15 102531392 79656523 0.7768988740541043 2.394029298743582 chr16 90354753 50552075 0.5594844025526803 1.9216078900700633 chr17 81195210 37687826 0.4641631692312884 1.9029021945883031 chr18 78077248 76140361 0.9751926835331082 2.867723058642169 chr19 59128983 24838892 0.4200798109448289 2.1502594191939854 chr20 63025520 51330728 0.8144435460429362 2.408453860707226 chr21 48129895 32435684 0.6739196917009688 2.008402816115889 chr22 51304566 13715710 0.26733897329917966 1.1575519095136897 chrMT 16571 1144 0.06903626817934946 0.3408344990846259 chrX 155270560 221362859 1.4256589207896204 3.8853744189057973 chrY 59373566 2119742 0.03570178014909867 0.552383648876165