BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004000.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 = 1,828,739 number of mapped reads = 1,438,726 (78.67%) number of supplementary alignments = 11,114 (0.61%) number of secondary alignments = 0 number of mapped bases = 91,138,436 bp number of sequenced bases = 91,087,714 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 109,201 duplication rate = 6.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5083 >>>>>>> ACTG content number of A's = 24,019,288 bp (26.37%) number of C's = 17,230,574 bp (18.92%) number of T's = 28,448,834 bp (31.23%) number of G's = 21,372,527 bp (23.46%) number of N's = 16,491 bp (0.02%) GC percentage = 42.38% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 915,768 number of insertions = 7,348 mapped reads with insertion percentage = 0.51% number of deletions = 31,402 mapped reads with deletion percentage = 2.15% homopolymer indels = 47.02% >>>>>>> Coverage mean coverageData = 0.0294X std coverageData = 0.288X There is a 2.13% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 8095333 0.03247868738509582 0.38998217775272653 chr2 243199373 7578690 0.031162456985446257 0.4069109947759683 chr3 198022430 5899614 0.029792655306775096 0.22635313942271196 chr4 191154276 5750371 0.03008235609649663 0.23161923807693244 chr5 180915260 5337253 0.029501397505108194 0.22563203133796578 chr6 171115067 5454650 0.031877087714315654 0.26185840354789247 chr7 159138663 5385119 0.033839162014324575 0.4030467330216933 chr8 146364022 5470024 0.03737273631357302 0.3113127408686715 chr9 141213431 3348172 0.023710010983303706 0.2438449643281042 chr10 135534747 4208116 0.031048244772242797 0.25818532956370294 chr11 135006516 3894924 0.028849896400555956 0.275432332786481 chr12 133851895 3760556 0.028094902952251817 0.22119803188607834 chr13 115169878 2606662 0.022633192335238906 0.19848797210502445 chr14 107349540 2481229 0.023113550370127342 0.21152975094491228 chr15 102531392 2510961 0.024489680194725142 0.20830473486853526 chr16 90354753 2650020 0.02932906030964414 0.23359917206398934 chr17 81195210 2459497 0.03029115880111647 0.24244966147594313 chr18 78077248 2537497 0.03249982632584591 0.3717195319469387 chr19 59128983 1804667 0.030520853030737902 0.3423358846993634 chr20 63025520 2177630 0.03455155943179842 0.24955603921598074 chr21 48129895 1329490 0.02762295658446793 0.22416766802892438 chr22 51304566 1129105 0.02200788522409487 0.19616887937387958 chrMT 16571 205455 12.398467201737976 8.242158346578954 chrX 155270560 4829645 0.031104705231951246 0.2432778155506294 chrY 59373566 233756 0.003937038243584695 0.08783192028842557