BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714218.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 = 183,516 number of mapped reads = 29,856 (16.27%) number of supplementary alignments = 895 (0.49%) number of secondary alignments = 0 number of mapped bases = 3,282,763 bp number of sequenced bases = 3,225,297 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,436 duplication rate = 38.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8596 >>>>>>> ACTG content number of A's = 786,997 bp (24.4%) number of C's = 532,427 bp (16.51%) number of T's = 728,593 bp (22.59%) number of G's = 1,177,257 bp (36.5%) number of N's = 23 bp (0%) GC percentage = 53.01% >>>>>>> Mismatches and indels general error rate = 0.0399 number of mismatches = 116,867 number of insertions = 3,456 mapped reads with insertion percentage = 10.64% number of deletions = 9,483 mapped reads with deletion percentage = 29.99% homopolymer indels = 28.65% >>>>>>> Coverage mean coverageData = 0.0011X std coverageData = 0.7343X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% 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 196660 7.890050552772745E-4 0.14239038636394993 chr2 243199373 870242 0.003578306922690956 2.569953133317928 chr3 198022430 173349 8.754008321178565E-4 0.14200896429778623 chr4 191154276 153662 8.038637859191808E-4 0.13996476433367278 chr5 180915260 174271 9.632741870420439E-4 0.15169043615873432 chr6 171115067 116918 6.832712165551149E-4 0.11776232209750431 chr7 159138663 93246 5.859418336322205E-4 0.14187030733079792 chr8 146364022 142972 9.768247554716692E-4 0.16919772592399654 chr9 141213431 100266 7.100316116531437E-4 0.13079645018219355 chr10 135534747 116108 8.56665929364962E-4 0.14550350116472568 chr11 135006516 114155 8.455517806266477E-4 0.16194400659093847 chr12 133851895 131214 9.802924344104356E-4 0.18811303426258277 chr13 115169878 75176 6.527401201206447E-4 0.13570745973692874 chr14 107349540 74772 6.965283689152278E-4 0.12089459132238149 chr15 102531392 94019 9.169776998638622E-4 0.15455151974065065 chr16 90354753 38813 4.295623496419718E-4 0.07698370515669298 chr17 81195210 51404 6.330915333552312E-4 0.11974330736920322 chr18 78077248 42490 5.442046318025963E-4 0.1277786603301399 chr19 59128983 18001 3.0443615104964685E-4 0.08814880136089924 chr20 63025520 51245 8.130833351315467E-4 0.137645026852063 chr21 48129895 24666 5.124881323759381E-4 0.09924259499206628 chr22 51304566 15793 3.0782835196383883E-4 0.08188055582109743 chrMT 16571 5946 0.35881962464546496 2.9876359291101093 chrX 155270560 401158 0.002583606319188905 0.2647585430975819 chrY 59373566 6217 1.0470989733040458E-4 0.05070551353975213