BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006099.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 = 14,364,604 number of mapped reads = 12,303,695 (85.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,267,551 number of mapped paired reads (second in pair) = 6,036,144 number of mapped paired reads (both in pair) = 11,011,148 number of mapped paired reads (singletons) = 1,292,547 number of mapped bases = 474,192,203 bp number of sequenced bases = 474,140,497 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,162,695 duplication rate = 15.58% >>>>>>> Insert size mean insert size = 84,632.2416 std insert size = 2,851,300.3116 median insert size = 110 >>>>>>> Mapping quality mean mapping quality = 46.4778 >>>>>>> ACTG content number of A's = 126,551,650 bp (26.69%) number of C's = 103,815,472 bp (21.9%) number of T's = 131,666,795 bp (27.77%) number of G's = 112,087,171 bp (23.64%) number of N's = 19,409 bp (0%) GC percentage = 45.54% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 2,514,515 number of insertions = 16,023 mapped reads with insertion percentage = 0.13% number of deletions = 41,082 mapped reads with deletion percentage = 0.33% homopolymer indels = 45.47% >>>>>>> Coverage mean coverageData = 0.1532X std coverageData = 1.0285X There is a 4.68% of reference with a coverageData >= 1X There is a 2.98% of reference with a coverageData >= 2X There is a 2.12% of reference with a coverageData >= 3X There is a 1.55% of reference with a coverageData >= 4X There is a 1.12% of reference with a coverageData >= 5X There is a 0.81% of reference with a coverageData >= 6X There is a 0.58% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.29% of reference with a coverageData >= 9X There is a 0.2% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.07% 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 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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% 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 40904769 0.16411100135232962 1.177294379472483 chr2 243199373 39563541 0.16267945312507034 1.0439315797511506 chr3 198022430 32604301 0.16464953490369752 0.9783844534820275 chr4 191154276 28453067 0.1488487079410141 0.9546825209330013 chr5 180915260 28433449 0.15716445920592878 0.9501766838352343 chr6 171115067 26777512 0.15648833541934679 1.0527982618843046 chr7 159138663 26356701 0.16562097797692318 1.1541646365186562 chr8 146364022 23678568 0.16177860977337724 1.1128918091982571 chr9 141213431 20317629 0.14387887084196688 0.9356217376235779 chr10 135534747 22779522 0.16807145403089882 1.0055267363243507 chr11 135006516 22501893 0.16667264415593097 1.4392662170590709 chr12 133851895 21791420 0.16280247657308103 0.9717726058564838 chr13 115169878 14323033 0.12436440194891932 0.8569798004297993 chr14 107349540 14705780 0.13698968807877518 0.9000089868614431 chr15 102531392 14748209 0.14384091264458793 0.9245727164718034 chr16 90354753 15596892 0.17261839009177524 1.0232999674247356 chr17 81195210 14886091 0.18333705892256452 1.1156676291989935 chr18 78077248 12473637 0.15976020312601183 1.0924919264299597 chr19 59128983 11189770 0.1892434036959506 1.2014175190272078 chr20 63025520 11728488 0.18609109452805783 1.070484355185908 chr21 48129895 6338276 0.13169104150341487 0.9279092533705398 chr22 51304566 6786450 0.13227770019533933 0.8947083779308755 chrMT 16571 6017 0.36310421821253996 1.4835947243538137 chrX 155270560 14240093 0.0917114809143472 0.7266145293010238 chrY 59373566 3007095 0.05064703373214942 0.5101401195190224