BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234062.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 5,690,941 number of mapped reads = 5,357,554 (94.14%) number of supplementary alignments = 54,182 (0.95%) number of secondary alignments = 0 number of mapped bases = 368,209,716 bp number of sequenced bases = 368,084,544 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 794,141 duplication rate = 6.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.3395 >>>>>>> ACTG content number of A's = 94,453,397 bp (25.66%) number of C's = 64,876,369 bp (17.63%) number of T's = 102,407,755 bp (27.82%) number of G's = 106,267,814 bp (28.87%) number of N's = 79,209 bp (0.02%) GC percentage = 46.5% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 2,119,696 number of insertions = 23,700 mapped reads with insertion percentage = 0.44% number of deletions = 75,761 mapped reads with deletion percentage = 1.4% homopolymer indels = 47.3% >>>>>>> Coverage mean coverageData = 0.1189X std coverageData = 65.9341X There is a 6.63% of reference with a coverageData >= 1X There is a 2.42% of reference with a coverageData >= 2X There is a 0.94% of reference with a coverageData >= 3X There is a 0.39% of reference with a coverageData >= 4X There is a 0.17% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% 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 64082196 0.2570994436960701 1.8318498921581547 chr2 243199373 52943047 0.21769401107789862 235.22296246480263 chr3 198022430 35057717 0.177039121275302 0.6326900268971701 chr4 191154276 19627928 0.10268108258274065 0.5026948058946852 chr5 180915260 30045688 0.16607602918626102 0.6126776583489565 chr6 171115067 26921076 0.15732732641246605 0.7575047033920006 chr7 159138663 13621686 0.08559633305452617 0.5520188529264929 chr8 146364022 4347836 0.029705633533355622 0.7653937458212406 chr9 141213431 15499537 0.10975965168638951 0.5383577706226628 chr10 135534747 17282261 0.12751166311617493 0.7499873983641072 chr11 135006516 3612362 0.026756945568464266 0.37379302712880835 chr12 133851895 9584755 0.07160716701097135 0.391915657717641 chr13 115169878 28322102 0.2459158808868409 0.7591741945813907 chr14 107349540 9455082 0.08807752692745587 0.5736567618610514 chr15 102531392 2264765 0.02208850339220987 0.21323761544337147 chr16 90354753 9186158 0.10166767873296051 0.4941231909424002 chr17 81195210 5130037 0.06318152265386098 0.3800472781348566 chr18 78077248 1129933 0.014471988049578796 0.7674204715544267 chr19 59128983 6412330 0.10844647877674474 1.058806571671662 chr20 63025520 7188574 0.11405814660474042 0.520198942244595 chr21 48129895 3007756 0.062492469597118384 0.3950755238496867 chr22 51304566 658305 0.012831314078360979 0.15405406260036986 chrMT 16571 63161 3.811538229436968 3.285237870572999 chrX 155270560 2290057 0.014748816517438978 0.21220875858250896 chrY 59373566 475367 0.008006374419215447 0.23356295548451486