BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714084.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 = 762,832 number of mapped reads = 41,261 (5.41%) number of supplementary alignments = 918 (0.12%) number of secondary alignments = 0 number of mapped bases = 3,249,580 bp number of sequenced bases = 3,223,696 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,757 duplication rate = 31.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 23.9339 >>>>>>> ACTG content number of A's = 342,275 bp (10.62%) number of C's = 197,364 bp (6.12%) number of T's = 266,167 bp (8.26%) number of G's = 2,417,832 bp (75%) number of N's = 58 bp (0%) GC percentage = 81.12% >>>>>>> Mismatches and indels general error rate = 0.0328 number of mismatches = 85,542 number of insertions = 3,873 mapped reads with insertion percentage = 7.15% number of deletions = 4,337 mapped reads with deletion percentage = 10.07% homopolymer indels = 43.58% >>>>>>> Coverage mean coverageData = 0.001X std coverageData = 2.561X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% 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 65591 2.63152804742661E-4 0.09437964060385323 chr2 243199373 2316487 0.009525053339672879 9.124104845978342 chr3 198022430 25349 1.280107511053167E-4 0.044826642305671016 chr4 191154276 23969 1.2539086491583374E-4 0.04554343312168754 chr5 180915260 53359 2.9493918865661196E-4 0.11931732545345448 chr6 171115067 49176 2.873855637738785E-4 0.11134924265547864 chr7 159138663 54437 3.420727494738347E-4 0.3416444020687435 chr8 146364022 41200 2.8148994156501113E-4 0.1025155527487295 chr9 141213431 38859 2.7517920728092784E-4 0.12689999493083098 chr10 135534747 47481 3.503234487905895E-4 0.11088701961969967 chr11 135006516 20612 1.5267411241098912E-4 0.08012389141832424 chr12 133851895 48309 3.6091382942318446E-4 0.14740569948754553 chr13 115169878 13726 1.1918046835128192E-4 0.06662108483672761 chr14 107349540 24148 2.2494740079929547E-4 0.11213025708307905 chr15 102531392 24377 2.3775157563451395E-4 0.09701809662112856 chr16 90354753 21755 2.407731666313116E-4 0.0924540687526287 chr17 81195210 15871 1.954671956633895E-4 0.09715783410743443 chr18 78077248 14652 1.876603027811636E-4 0.060475973321656204 chr19 59128983 4371 7.392313850552782E-5 0.022247771250060687 chr20 63025520 8987 1.425930321558632E-4 0.03582718116679694 chr21 48129895 10161 2.1111618880531528E-4 0.06464891436234788 chr22 51304566 2347 4.574641563092065E-5 0.011929980284000139 chrMT 16571 9895 0.5971275119184117 5.530228642148487 chrX 155270560 311346 0.0020051837257494274 0.33178954175698105 chrY 59373566 3115 5.2464424993439E-5 0.026710726836516784