BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231798.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 = 3,111,684 number of mapped reads = 1,816,430 (58.37%) number of supplementary alignments = 11,948 (0.38%) number of secondary alignments = 0 number of mapped bases = 118,447,706 bp number of sequenced bases = 118,404,053 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 164,429 duplication rate = 2.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7681 >>>>>>> ACTG content number of A's = 34,505,192 bp (29.14%) number of C's = 20,728,292 bp (17.51%) number of T's = 31,266,112 bp (26.41%) number of G's = 31,896,669 bp (26.94%) number of N's = 7,788 bp (0.01%) GC percentage = 44.45% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 843,961 number of insertions = 8,824 mapped reads with insertion percentage = 0.48% number of deletions = 26,345 mapped reads with deletion percentage = 1.44% homopolymer indels = 43.92% >>>>>>> Coverage mean coverageData = 0.0383X std coverageData = 16.0424X There is a 3.24% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 10375674 0.0416274750224193 0.6168182930743906 chr2 243199373 15658674 0.06438616106136096 57.224797947683534 chr3 198022430 11806232 0.059620680344140815 0.26111073590442735 chr4 191154276 3629708 0.0189883693734374 0.15322420415280572 chr5 180915260 5405458 0.029878397212042808 0.1852911248578207 chr6 171115067 6919334 0.04043673138380035 0.25162348392519557 chr7 159138663 6177041 0.03881546371920946 0.3794240008577858 chr8 146364022 5909048 0.040372271267593345 0.566871120892127 chr9 141213431 4154222 0.029418037438662614 0.23429810246544808 chr10 135534747 6116796 0.045130832759808816 0.29452275323570604 chr11 135006516 5636251 0.04174799237097564 0.3041019843377002 chr12 133851895 3930558 0.029364978359103545 0.1853603449775274 chr13 115169878 4259174 0.03698166633466435 0.2049240281057167 chr14 107349540 5930664 0.05524629169347162 0.3742115650793353 chr15 102531392 2914464 0.028425089556962223 0.18185140817915474 chr16 90354753 2501582 0.02768622476340564 0.1926536858658027 chr17 81195210 2563029 0.03156625864998686 0.21031076614287145 chr18 78077248 2206926 0.028265929659815878 0.4200097601301177 chr19 59128983 2766476 0.046787139903962154 0.3911949421057298 chr20 63025520 2747575 0.04359464229727894 0.22738202853210193 chr21 48129895 1931735 0.04013586566104081 0.22069399494414849 chr22 51304566 947617 0.018470422301204145 0.14402060304727543 chrMT 16571 81318 4.907247601231067 3.6642205100951526 chrX 155270560 3657970 0.02355868362940148 0.18250704055053185 chrY 59373566 220180 0.0037083843001782983 0.07992134274658226