BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714107.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 605,996 number of mapped reads = 364,406 (60.13%) number of supplementary alignments = 11,211 (1.85%) number of secondary alignments = 0 number of mapped bases = 47,311,130 bp number of sequenced bases = 46,234,927 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 311,400 duplication rate = 43.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.4669 >>>>>>> ACTG content number of A's = 12,545,339 bp (27.13%) number of C's = 9,408,914 bp (20.35%) number of T's = 11,977,109 bp (25.9%) number of G's = 12,303,115 bp (26.61%) number of N's = 450 bp (0%) GC percentage = 46.96% >>>>>>> Mismatches and indels general error rate = 0.0465 number of mismatches = 1,986,809 number of insertions = 52,181 mapped reads with insertion percentage = 13.65% number of deletions = 179,449 mapped reads with deletion percentage = 45.66% homopolymer indels = 30.67% >>>>>>> Coverage mean coverageData = 0.0153X std coverageData = 4.1975X There is a 0.05% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% 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 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3085964 0.012380968150125491 1.7762211830122439 chr2 243199373 7382846 0.030357175304066265 12.4868402630245 chr3 198022430 2154029 0.010877702086576757 2.341561485760002 chr4 191154276 1961084 0.010259168881997701 1.8083130804033978 chr5 180915260 2488103 0.013752864186249408 2.106501562550303 chr6 171115067 2114756 0.012358677918175376 2.5026652053644938 chr7 159138663 2161373 0.013581696359985128 2.4267913861775345 chr8 146364022 2390503 0.016332586159732616 3.392116190685618 chr9 141213431 1491391 0.010561254616071186 1.662744813075337 chr10 135534747 2591081 0.01911746660802783 3.5330547058551622 chr11 135006516 1842298 0.013645993205246478 1.9142339064255325 chr12 133851895 2146239 0.016034431189786293 2.671750766816091 chr13 115169878 1002559 0.008705045254975436 1.1899070848626159 chr14 107349540 1348527 0.0125620193621696 2.123544101632863 chr15 102531392 1378097 0.01344073237589518 1.764550480899045 chr16 90354753 1019889 0.011287607636977327 1.5061977137921903 chr17 81195210 1575063 0.01939847190493134 4.119212660946299 chr18 78077248 1149105 0.014717539737056307 2.059014347388521 chr19 59128983 1018870 0.01723131277262117 3.393057809816634 chr20 63025520 850112 0.013488377406485499 1.8468225892209822 chr21 48129895 359272 0.007464632947983784 1.839853392523384 chr22 51304566 370709 0.007225653170908804 0.9718102314670787 chrMT 16571 516083 31.14374509685595 239.54261675315988 chrX 155270560 4685958 0.030179307654973356 2.6825371094433437 chrY 59373566 227219 0.0038269387424026374 0.655536376595611