BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237320.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 = 2,286,486 number of mapped reads = 1,929,655 (84.39%) number of supplementary alignments = 19,374 (0.85%) number of secondary alignments = 0 number of mapped bases = 118,672,112 bp number of sequenced bases = 118,613,745 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 599,039 duplication rate = 20.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9498 >>>>>>> ACTG content number of A's = 29,560,485 bp (24.92%) number of C's = 20,440,825 bp (17.23%) number of T's = 39,836,108 bp (33.58%) number of G's = 28,764,667 bp (24.25%) number of N's = 11,660 bp (0.01%) GC percentage = 41.48% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 786,793 number of insertions = 9,394 mapped reads with insertion percentage = 0.48% number of deletions = 33,213 mapped reads with deletion percentage = 1.7% homopolymer indels = 43.34% >>>>>>> Coverage mean coverageData = 0.0383X std coverageData = 0.6018X There is a 1.71% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% 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% 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 11385757 0.04567995439417581 0.6417330932736685 chr2 243199373 9071155 0.03729925323450567 1.2268375765890462 chr3 198022430 9030538 0.0456036116716677 0.4056687837411539 chr4 191154276 4739174 0.024792403806860173 0.38920544740110286 chr5 180915260 4161003 0.02299973479296329 0.30235104265806145 chr6 171115067 11303580 0.0660583559249052 0.6133108039252096 chr7 159138663 7455379 0.04684831994598321 0.5904585495633268 chr8 146364022 6443952 0.04402688524096448 0.8868574209169968 chr9 141213431 4404371 0.031189462424434683 0.3991167927627393 chr10 135534747 5121475 0.037787173498763385 0.5432473525625355 chr11 135006516 4146983 0.030716909989737088 0.3808392826255771 chr12 133851895 3380567 0.025256026446244934 0.3252749876644283 chr13 115169878 4237280 0.03679156454433337 0.4227680179637271 chr14 107349540 5753411 0.053595115544975785 0.43432137843855206 chr15 102531392 2555049 0.024919675332214352 0.311930377725463 chr16 90354753 3166754 0.03504800682704539 0.37084049143387066 chr17 81195210 4166001 0.051308457727986666 0.4805174876137246 chr18 78077248 3371805 0.04318550008319966 1.0827249981956575 chr19 59128983 2585431 0.04372527428723068 0.48543115318776453 chr20 63025520 2429511 0.038548051646380706 0.39259478597047814 chr21 48129895 2374790 0.04934126700255631 0.4477540810116392 chr22 51304566 1204879 0.023484829790783143 0.30553439570539953 chrMT 16571 17967 1.0842435580230523 2.4713867296309178 chrX 155270560 5671782 0.036528379880899506 0.40507799910760295 chrY 59373566 493518 0.008312082855188451 0.306927421672031