BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008714.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 = 1,345,377 number of mapped reads = 1,244,585 (92.51%) number of supplementary alignments = 6,159 (0.46%) number of secondary alignments = 0 number of mapped bases = 81,787,146 bp number of sequenced bases = 81,741,809 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,107 duplication rate = 2.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9593 >>>>>>> ACTG content number of A's = 22,006,327 bp (26.92%) number of C's = 15,537,831 bp (19.01%) number of T's = 25,249,938 bp (30.89%) number of G's = 18,841,591 bp (23.05%) number of N's = 106,122 bp (0.13%) GC percentage = 42.06% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 681,385 number of insertions = 5,603 mapped reads with insertion percentage = 0.45% number of deletions = 25,441 mapped reads with deletion percentage = 2.02% homopolymer indels = 44.87% >>>>>>> Coverage mean coverageData = 0.0264X std coverageData = 0.277X There is a 2.33% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% 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 8308452 0.03333372637815815 0.43148225807962487 chr2 243199373 8503345 0.03496450214943605 0.3268989492013199 chr3 198022430 6016665 0.030383755011995358 0.2118244397827813 chr4 191154276 3666675 0.01918175767096102 0.1605126064898323 chr5 180915260 2649308 0.01464391671548326 0.13230232395491565 chr6 171115067 4362911 0.025496942358676108 0.19250213738116842 chr7 159138663 5478628 0.0344267564947432 0.4084194281640711 chr8 146364022 6151055 0.04202573088624197 0.3357550366559098 chr9 141213431 984298 0.006970285992130593 0.16489984288564613 chr10 135534747 5817971 0.042926047591323575 0.530490624377183 chr11 135006516 5202045 0.03853180686478866 0.2852536806165705 chr12 133851895 3989991 0.02980899896859884 0.18878183893890532 chr13 115169878 1918595 0.016658826364303346 0.13982053602658584 chr14 107349540 2551896 0.02377183917136487 0.17191917400880838 chr15 102531392 757832 0.007391219266778315 0.0957672116461912 chr16 90354753 2514205 0.02782592964423244 0.2383866870164915 chr17 81195210 1997074 0.024595958308378043 0.19742420419520548 chr18 78077248 1207559 0.015466208542596173 0.336061697711373 chr19 59128983 1939050 0.03279356250723947 0.3118102864166759 chr20 63025520 2244432 0.03561147928648586 0.2104308563413964 chr21 48129895 998994 0.020756205680481955 0.1650602043032776 chr22 51304566 965124 0.018811658985673906 0.14973291691211088 chrMT 16571 14370 0.8671775994206746 1.1930762283896144 chrX 155270560 3302574 0.021269801564443382 0.1751683612606668 chrY 59373566 244097 0.004111206660553284 0.15474069923016717