BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006188.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 9,533,036 number of mapped reads = 8,371,928 (87.82%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,222,188 number of mapped paired reads (second in pair) = 4,149,740 number of mapped paired reads (both in pair) = 7,743,666 number of mapped paired reads (singletons) = 628,262 number of mapped bases = 324,003,282 bp number of sequenced bases = 323,962,862 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 315,869 duplication rate = 3.11% >>>>>>> Insert size mean insert size = 60,056.5956 std insert size = 2,338,215.4215 median insert size = 112 >>>>>>> Mapping quality mean mapping quality = 47.6652 >>>>>>> ACTG content number of A's = 88,157,070 bp (27.21%) number of C's = 71,774,005 bp (22.16%) number of T's = 89,957,994 bp (27.77%) number of G's = 74,035,763 bp (22.85%) number of N's = 38,030 bp (0.01%) GC percentage = 45.01% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 1,021,835 number of insertions = 9,375 mapped reads with insertion percentage = 0.11% number of deletions = 30,290 mapped reads with deletion percentage = 0.36% homopolymer indels = 43.14% >>>>>>> Coverage mean coverageData = 0.1047X std coverageData = 0.5622X There is a 8.12% of reference with a coverageData >= 1X There is a 1.67% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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% 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 26961071 0.10816852087201019 0.7229153678770381 chr2 243199373 27075380 0.11132997452259057 0.5163793028396924 chr3 198022430 21543500 0.10879323115063279 0.39928193529287886 chr4 191154276 19687471 0.10299257443762336 0.46108459713314 chr5 180915260 19193546 0.10609136012075487 0.3981798528446699 chr6 171115067 17869849 0.10443176812711648 0.441501783446526 chr7 159138663 17575811 0.11044337478190325 0.606724955871568 chr8 146364022 16125839 0.11017624946108683 1.1067243130393138 chr9 141213431 13427607 0.09508732211173312 0.44945696197448837 chr10 135534747 15399973 0.1136238001019768 0.5874365592095799 chr11 135006516 14781268 0.10948558956961751 0.48466421857486336 chr12 133851895 14475378 0.10814473713651944 0.407805085633049 chr13 115169878 9735125 0.0845283955236976 0.35249083546847176 chr14 107349540 10155248 0.09459982781481877 0.9125578274798447 chr15 102531392 9669372 0.09430645396875134 0.3783494986463153 chr16 90354753 10231120 0.11323278145644425 0.489785659575289 chr17 81195210 9627078 0.11856706818049981 0.4419936952774251 chr18 78077248 8466318 0.10843514873884899 0.6800311300170732 chr19 59128983 7482120 0.12653895975176843 0.6117224862637388 chr20 63025520 7473683 0.11858185382683079 0.4439082846832347 chr21 48129895 4260569 0.0885222999135984 0.4517741067982558 chr22 51304566 4592121 0.08950706258776266 0.40906439479002693 chrMT 16571 5744 0.3466296542151952 1.087920610603012 chrX 155270560 17349066 0.11173442022750482 0.4365392289227788 chrY 59373566 839025 0.014131288661354786 0.330928100425863