BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089596.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 = 23,688,972 number of mapped reads = 18,776,767 (79.26%) number of supplementary alignments = 726 (0%) number of secondary alignments = 0 number of mapped bases = 878,932,188 bp number of sequenced bases = 878,752,648 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,850,950 duplication rate = 7.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7414 >>>>>>> ACTG content number of A's = 280,511,717 bp (31.92%) number of C's = 178,514,505 bp (20.31%) number of T's = 223,422,329 bp (25.42%) number of G's = 195,906,224 bp (22.29%) number of N's = 397,873 bp (0.05%) GC percentage = 42.61% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 4,977,979 number of insertions = 40,206 mapped reads with insertion percentage = 0.21% number of deletions = 118,297 mapped reads with deletion percentage = 0.63% homopolymer indels = 43.23% >>>>>>> Coverage mean coverageData = 0.2839X std coverageData = 1.3801X There is a 15.07% of reference with a coverageData >= 1X There is a 5.94% of reference with a coverageData >= 2X There is a 2.81% of reference with a coverageData >= 3X There is a 1.5% of reference with a coverageData >= 4X There is a 0.87% of reference with a coverageData >= 5X There is a 0.54% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.25% of reference with a coverageData >= 8X There is a 0.17% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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% 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 68902636 0.2764391748496386 1.8041812404774589 chr2 243199373 74243959 0.3052802237282084 1.551288858363848 chr3 198022430 58052673 0.29316210794908437 0.971193824872556 chr4 191154276 58274006 0.3048532694084228 1.0939221505791352 chr5 180915260 55922777 0.3091103370716213 1.0108670020026576 chr6 171115067 50407646 0.2945833285388013 1.1301279311142591 chr7 159138663 48407494 0.3041843703311746 1.6636485791150522 chr8 146364022 44873404 0.30658766674230914 2.7131838352562925 chr9 141213431 36420462 0.2579107507132236 1.2226544577612526 chr10 135534747 41217342 0.3041090414991515 1.4385685679041411 chr11 135006516 39015717 0.28899136246134965 1.2467985686491683 chr12 133851895 40358235 0.3015141100542506 1.0137033559607043 chr13 115169878 28081053 0.24382289438563093 0.8903633749448018 chr14 107349540 26614989 0.24792830039141295 1.040574645860855 chr15 102531392 25071897 0.24452898288945496 0.8955190628850155 chr16 90354753 24765770 0.27409482265974433 1.0762713755904199 chr17 81195210 23421568 0.28845997196140016 1.0801486157463045 chr18 78077248 23277163 0.29812991103374953 1.713408639319293 chr19 59128983 17686534 0.2991178454735134 1.7674405126873358 chr20 63025520 17923172 0.28437959734406 1.0585286164160934 chr21 48129895 11363031 0.23609091605124008 1.0860468720366192 chr22 51304566 10052715 0.1959419167486964 0.8187683253467736 chrMT 16571 151331 9.132279283084907 9.532445226556018 chrX 155270560 51829403 0.3338005800970899 1.2094449642823148 chrY 59373566 2597211 0.04374355752861467 0.6333681714168268