BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618616.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 35,972,054 number of mapped reads = 30,325,080 (84.3%) number of supplementary alignments = 52,172 (0.15%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,354,130 number of mapped paired reads (second in pair) = 14,970,950 number of mapped paired reads (both in pair) = 29,324,382 number of mapped paired reads (singletons) = 1,000,698 number of mapped bases = 2,896,502,352 bp number of sequenced bases = 2,894,669,850 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,355,081 duplication rate = 21.27% >>>>>>> Insert size mean insert size = 37,036.0014 std insert size = 1,916,011.1805 median insert size = 216 >>>>>>> Mapping quality mean mapping quality = 52.5302 >>>>>>> ACTG content number of A's = 773,961,904 bp (26.74%) number of C's = 655,291,347 bp (22.64%) number of T's = 778,404,415 bp (26.89%) number of G's = 686,851,764 bp (23.73%) number of N's = 160,420 bp (0.01%) GC percentage = 46.37% >>>>>>> Mismatches and indels general error rate = 0.0119 number of mismatches = 33,541,294 number of insertions = 503,754 mapped reads with insertion percentage = 1.63% number of deletions = 1,318,724 mapped reads with deletion percentage = 4.25% homopolymer indels = 52.44% >>>>>>> Coverage mean coverageData = 0.9357X std coverageData = 4.2049X There is a 19.94% of reference with a coverageData >= 1X There is a 13.07% of reference with a coverageData >= 2X There is a 9.4% of reference with a coverageData >= 3X There is a 7.16% of reference with a coverageData >= 4X There is a 5.63% of reference with a coverageData >= 5X There is a 4.55% of reference with a coverageData >= 6X There is a 3.75% of reference with a coverageData >= 7X There is a 3.14% of reference with a coverageData >= 8X There is a 2.66% of reference with a coverageData >= 9X There is a 2.28% of reference with a coverageData >= 10X There is a 1.97% of reference with a coverageData >= 11X There is a 1.72% of reference with a coverageData >= 12X There is a 1.51% of reference with a coverageData >= 13X There is a 1.33% of reference with a coverageData >= 14X There is a 1.18% of reference with a coverageData >= 15X There is a 1.06% of reference with a coverageData >= 16X There is a 0.95% of reference with a coverageData >= 17X There is a 0.85% of reference with a coverageData >= 18X There is a 0.77% of reference with a coverageData >= 19X There is a 0.7% of reference with a coverageData >= 20X There is a 0.64% of reference with a coverageData >= 21X There is a 0.58% of reference with a coverageData >= 22X There is a 0.53% of reference with a coverageData >= 23X There is a 0.49% of reference with a coverageData >= 24X There is a 0.45% of reference with a coverageData >= 25X There is a 0.41% of reference with a coverageData >= 26X There is a 0.38% of reference with a coverageData >= 27X There is a 0.35% of reference with a coverageData >= 28X There is a 0.32% of reference with a coverageData >= 29X There is a 0.3% of reference with a coverageData >= 30X There is a 0.28% of reference with a coverageData >= 31X There is a 0.26% of reference with a coverageData >= 32X There is a 0.24% of reference with a coverageData >= 33X There is a 0.23% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.14% of reference with a coverageData >= 41X There is a 0.13% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.12% of reference with a coverageData >= 44X There is a 0.11% of reference with a coverageData >= 45X There is a 0.11% of reference with a coverageData >= 46X There is a 0.1% of reference with a coverageData >= 47X There is a 0.09% of reference with a coverageData >= 48X There is a 0.09% of reference with a coverageData >= 49X There is a 0.08% of reference with a coverageData >= 50X There is a 0.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 271686077 1.090011635317049 4.9401205882394095 chr2 243199373 241305825 0.9922140095320064 4.742637026901492 chr3 198022430 187048314 0.9445814496872905 3.6582813599228015 chr4 191154276 132582938 0.6935912749343885 3.3415442802752366 chr5 180915260 170846570 0.9443458224585367 3.6945739186736026 chr6 171115067 149186921 0.8718514600470572 3.5208022946939024 chr7 159138663 147201004 0.9249858031043028 3.6259288833760484 chr8 146364022 141273481 0.9652199978489249 3.7237990899587095 chr9 141213431 128213805 0.907943416515388 4.188525078726333 chr10 135534747 156009771 1.1510684488900842 4.352907330502289 chr11 135006516 163489172 1.2109724540999192 4.7588601256552545 chr12 133851895 139176708 1.039781379262505 4.092362607282833 chr13 115169878 72031258 0.6254348728232568 2.7125824395554514 chr14 107349540 93791585 0.8737027191732727 3.7422877345482557 chr15 102531392 100731608 0.9824465076998077 4.052156938951507 chr16 90354753 116066407 1.284563380965692 7.242870350655451 chr17 81195210 107519390 1.324208533976327 5.054523283007028 chr18 78077248 77177033 0.9884702006914998 4.165479398125021 chr19 59128983 75203264 1.2718511326332131 5.094920607664395 chr20 63025520 94583374 1.500715487948374 4.97634818209437 chr21 48129895 39104576 0.8124799773612638 6.046555669258609 chr22 51304566 62327983 1.2148622990008335 4.975903211068974 chrMT 16571 174038 10.502564721501418 31.435265275093368 chrX 155270560 4354932 0.02804737742943672 0.8527889792371767 chrY 59373566 25416318 0.4280746418364024 3.2680895917052775