BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089756.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 21,106,029 number of mapped reads = 19,372,062 (91.78%) number of supplementary alignments = 140,394 (0.67%) number of secondary alignments = 0 number of mapped bases = 1,284,874,078 bp number of sequenced bases = 1,284,391,830 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,154,934 duplication rate = 15.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1466 >>>>>>> ACTG content number of A's = 342,820,158 bp (26.69%) number of C's = 236,891,682 bp (18.44%) number of T's = 405,456,711 bp (31.57%) number of G's = 298,413,400 bp (23.23%) number of N's = 809,879 bp (0.06%) GC percentage = 41.68% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 8,373,575 number of insertions = 83,468 mapped reads with insertion percentage = 0.43% number of deletions = 269,025 mapped reads with deletion percentage = 1.37% homopolymer indels = 48.1% >>>>>>> Coverage mean coverageData = 0.4151X std coverageData = 2.5413X There is a 13.11% of reference with a coverageData >= 1X There is a 8.1% of reference with a coverageData >= 2X There is a 5.44% of reference with a coverageData >= 3X There is a 3.8% of reference with a coverageData >= 4X There is a 2.71% of reference with a coverageData >= 5X There is a 1.95% of reference with a coverageData >= 6X There is a 1.42% of reference with a coverageData >= 7X There is a 1.05% of reference with a coverageData >= 8X There is a 0.77% of reference with a coverageData >= 9X There is a 0.58% of reference with a coverageData >= 10X There is a 0.43% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.25% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% 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 104926845 0.4209692420385183 3.8669635152256734 chr2 243199373 132920368 0.5465489748610495 2.775553871217196 chr3 198022430 116318841 0.5874023513396942 1.8847058674541752 chr4 191154276 66977815 0.3503861718479162 1.6114275830351055 chr5 180915260 62683095 0.3464776547871086 1.4069452789594463 chr6 171115067 71012963 0.4150012283839389 1.6821556080134095 chr7 159138663 92573838 0.5817180831788187 3.330942404169771 chr8 146364022 106957417 0.7307630354678283 5.971945094455047 chr9 141213431 40725547 0.28839712137579887 1.8462442352906194 chr10 135534747 39837282 0.29392670796072684 1.9052439790570725 chr11 135006516 55183931 0.4087501302529724 2.082338293508516 chr12 133851895 45603523 0.34070136250218946 1.424579204349799 chr13 115169878 37382641 0.3245869636156079 1.3590564504113902 chr14 107349540 47723360 0.4445604517727789 1.6579017304368544 chr15 102531392 33358207 0.32534628028847984 1.3727393708014297 chr16 90354753 25042432 0.27715677558213236 1.3493576739260955 chr17 81195210 24053895 0.29624770968632264 1.5618821432583554 chr18 78077248 49182082 0.6299156701834573 3.540911513058493 chr19 59128983 21568915 0.3647773715303035 2.392501207608534 chr20 63025520 28916347 0.4588037829755312 1.741374912298621 chr21 48129895 19598799 0.4072063527252657 1.7376944023514855 chr22 51304566 10590538 0.20642486284749004 1.1066485277365095 chrMT 16571 1674667 101.06010500271559 55.6119403669971 chrX 155270560 46332010 0.29839533006128144 1.429136871695514 chrY 59373566 3728720 0.06280101148042885 1.6482695299663892