BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549141.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 12,930,174 number of mapped reads = 11,429,842 (88.4%) number of secondary alignments = 0 number of mapped bases = 453,650,868 bp number of sequenced bases = 453,604,150 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 593,078 duplication rate = 4.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.4268 >>>>>>> ACTG content number of A's = 127,136,350 bp (28.03%) number of C's = 98,957,568 bp (21.82%) number of T's = 128,548,434 bp (28.34%) number of G's = 98,861,619 bp (21.79%) number of N's = 100,179 bp (0.02%) GC percentage = 43.61% >>>>>>> Mismatches and indels general error rate = 0.0033 number of mismatches = 1,469,018 number of insertions = 12,343 mapped reads with insertion percentage = 0.11% number of deletions = 36,819 mapped reads with deletion percentage = 0.32% homopolymer indels = 46.73% >>>>>>> Coverage mean coverageData = 0.1465X std coverageData = 0.8021X There is a 10.43% of reference with a coverageData >= 1X There is a 2.73% of reference with a coverageData >= 2X There is a 0.83% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 37953970 0.15227231871169541 1.2357110257397932 chr2 243199373 38273839 0.15737638846626467 0.8503410123504739 chr3 198022430 29944140 0.15121590013818131 0.5189614747445478 chr4 191154276 26914208 0.1407983570296905 0.5168084001318126 chr5 180915260 27026624 0.14938830477871243 0.536442137749506 chr6 171115067 25926878 0.1515172126835564 0.6167179697056955 chr7 159138663 25790793 0.16206490939288587 1.3715493003578119 chr8 146364022 22719977 0.1552292475264174 0.7846929560313224 chr9 141213431 19565012 0.13854922907439307 0.8095376690384467 chr10 135534747 22336623 0.16480366470156912 0.7097146205201615 chr11 135006516 20993744 0.1555017092656476 0.709915500717922 chr12 133851895 21080602 0.15749199516375917 0.558475552719113 chr13 115169878 13569750 0.11782377680386186 0.45271090943008646 chr14 107349540 14123687 0.13156728012062277 0.625546828983276 chr15 102531392 14375646 0.14020726452245963 0.49674681245483393 chr16 90354753 15106301 0.16718878087132838 0.6088468664023498 chr17 81195210 14589323 0.17968206498880906 0.6084164684959442 chr18 78077248 11877650 0.1521269038580868 1.60963744612496 chr19 59128983 11119800 0.18806005846574428 1.2284283140523555 chr20 63025520 10780035 0.17104238092759885 0.5889873472946446 chr21 48129895 5920323 0.12300718711312376 0.5863490583133532 chr22 51304566 6657966 0.12977336169260256 0.5567835277818715 chrMT 16571 97358 5.875203669060407 10.11362614778296 chrX 155270560 13971334 0.0899805732651444 0.531883829724241 chrY 59373566 2935285 0.04943757294281432 0.3091072458701914