BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716737.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 407,316 number of mapped reads = 374,292 (91.89%) number of supplementary alignments = 2,310 (0.57%) number of secondary alignments = 0 number of mapped bases = 22,423,844 bp number of sequenced bases = 22,417,106 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,589 duplication rate = 1.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2679 >>>>>>> ACTG content number of A's = 5,909,842 bp (26.36%) number of C's = 4,643,252 bp (20.71%) number of T's = 6,732,051 bp (30.03%) number of G's = 5,131,603 bp (22.89%) number of N's = 358 bp (0%) GC percentage = 43.6% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 106,912 number of insertions = 1,753 mapped reads with insertion percentage = 0.47% number of deletions = 4,176 mapped reads with deletion percentage = 1.11% homopolymer indels = 39.59% >>>>>>> Coverage mean coverageData = 0.0072X std coverageData = 0.1026X There is a 0.69% of reference with a coverageData >= 1X There is a 0.02% 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 1835312 0.007363319668519502 0.12313779891742165 chr2 243199373 2252882 0.009263518948299262 0.11670730327754242 chr3 198022430 1653270 0.00834890269753785 0.09492447020146608 chr4 191154276 1247348 0.00652534709712693 0.0866813656931164 chr5 180915260 1106113 0.006113983972385746 0.08044354658563484 chr6 171115067 1194021 0.006977883484684607 0.08720165255534731 chr7 159138663 1366324 0.008585745124677841 0.17160913358086588 chr8 146364022 1763447 0.012048363907354226 0.12671792605920296 chr9 141213431 961758 0.006810669446874355 0.08878175802105201 chr10 135534747 1099596 0.008113019165483815 0.13035147535013014 chr11 135006516 792882 0.0058729165338952975 0.08249277702218223 chr12 133851895 1009742 0.007543725847138735 0.09247743517445549 chr13 115169878 562223 0.004881684427936964 0.07180012538424246 chr14 107349540 557765 0.005195783791900738 0.07362217189337465 chr15 102531392 525473 0.005124996254805552 0.07319152940783669 chr16 90354753 679399 0.007519239192652101 0.09121751781251099 chr17 81195210 942711 0.011610426280072432 0.11145871506097178 chr18 78077248 510378 0.006536833880210532 0.10758345100431091 chr19 59128983 452680 0.007655805613974453 0.11040510854901361 chr20 63025520 497193 0.007888756808353188 0.09265626380181655 chr21 48129895 235806 0.004899366599490815 0.07639673468380646 chr22 51304566 350730 0.00683623364049118 0.08440025067676714 chrMT 16571 13975 0.8433407760545532 1.0352379551569846 chrX 155270560 757692 0.0048798175262586806 0.07431031465756974 chrY 59373566 55124 9.284266334954515E-4 0.04044390307254837