BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR960911.sorted.bam
outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 130,591,606
number of mapped reads = 124,119,392 (95.04%)
number of supplementary alignments = 2,027,303 (1.55%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 62,286,071
number of mapped paired reads (second in pair) = 61,833,321
number of mapped paired reads (both in pair) = 121,521,958
number of mapped paired reads (singletons) = 2,597,434
number of mapped bases = 10,834,817,578 bp
number of sequenced bases = 10,831,842,235 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 13,729,006
duplication rate = 5.63%
>>>>>>> Insert size
mean insert size = 156,552.6569
std insert size = 4,092,208.8058
median insert size = 149
>>>>>>> Mapping quality
mean mapping quality = 52.3792
>>>>>>> ACTG content
number of A's = 3,145,842,593 bp (29.04%)
number of C's = 2,224,224,651 bp (20.53%)
number of T's = 3,207,137,336 bp (29.61%)
number of G's = 2,253,206,918 bp (20.8%)
number of N's = 1,430,737 bp (0.01%)
GC percentage = 41.34%
>>>>>>> Mismatches and indels
general error rate = 0.016
number of mismatches = 169,613,332
number of insertions = 1,668,734
mapped reads with insertion percentage = 1.32%
number of deletions = 1,399,578
mapped reads with deletion percentage = 1.1%
homopolymer indels = 37.06%
>>>>>>> Coverage
mean coverageData = 3.5X
std coverageData = 48.0037X
There is a 83.22% of reference with a coverageData >= 1X
There is a 70.26% of reference with a coverageData >= 2X
There is a 54.89% of reference with a coverageData >= 3X
There is a 40.56% of reference with a coverageData >= 4X
There is a 28.51% of reference with a coverageData >= 5X
There is a 19.31% of reference with a coverageData >= 6X
There is a 12.67% of reference with a coverageData >= 7X
There is a 8.13% of reference with a coverageData >= 8X
There is a 5.14% of reference with a coverageData >= 9X
There is a 3.22% of reference with a coverageData >= 10X
There is a 2.02% of reference with a coverageData >= 11X
There is a 1.29% of reference with a coverageData >= 12X
There is a 0.84% of reference with a coverageData >= 13X
There is a 0.56% of reference with a coverageData >= 14X
There is a 0.39% of reference with a coverageData >= 15X
There is a 0.29% of reference with a coverageData >= 16X
There is a 0.23% of reference with a coverageData >= 17X
There is a 0.18% of reference with a coverageData >= 18X
There is a 0.16% of reference with a coverageData >= 19X
There is a 0.14% of reference with a coverageData >= 20X
There is a 0.12% of reference with a coverageData >= 21X
There is a 0.11% of reference with a coverageData >= 22X
There is a 0.1% of reference with a coverageData >= 23X
There is a 0.09% of reference with a coverageData >= 24X
There is a 0.09% of reference with a coverageData >= 25X
There is a 0.08% of reference with a coverageData >= 26X
There is a 0.08% of reference with a coverageData >= 27X
There is a 0.07% of reference with a coverageData >= 28X
There is a 0.07% of reference with a coverageData >= 29X
There is a 0.06% of reference with a coverageData >= 30X
There is a 0.06% of reference with a coverageData >= 31X
There is a 0.06% of reference with a coverageData >= 32X
There is a 0.06% of reference with a coverageData >= 33X
There is a 0.05% of reference with a coverageData >= 34X
There is a 0.05% of reference with a coverageData >= 35X
There is a 0.05% of reference with a coverageData >= 36X
There is a 0.05% of reference with a coverageData >= 37X
There is a 0.05% of reference with a coverageData >= 38X
There is a 0.04% of reference with a coverageData >= 39X
There is a 0.04% of reference with a coverageData >= 40X
There is a 0.04% of reference with a coverageData >= 41X
There is a 0.04% of reference with a coverageData >= 42X
There is a 0.04% of reference with a coverageData >= 43X
There is a 0.04% of reference with a coverageData >= 44X
There is a 0.04% of reference with a coverageData >= 45X
There is a 0.04% of reference with a coverageData >= 46X
There is a 0.04% of reference with a coverageData >= 47X
There is a 0.04% of reference with a coverageData >= 48X
There is a 0.03% of reference with a coverageData >= 49X
There is a 0.03% of reference with a coverageData >= 50X
There is a 0.03% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 1000980674 4.015960602160345 121.01606185351841
chr2 243199373 940235239 3.866108811884149 69.28972212667819
chr3 198022430 748040420 3.7775539871922588 7.998244139314886
chr4 191154276 656202141 3.4328405031337095 21.562391161075023
chr5 180915260 528858085 2.9232364644088067 4.771599998659239
chr6 171115067 540782336 3.1603431859100986 14.866078705782087
chr7 159138663 613520286 3.8552560040045076 31.27092955005317
chr8 146364022 562925854 3.846067129803252 39.389988056689965
chr9 141213431 516868790 3.660195679262265 36.81379321784264
chr10 135534747 524773148 3.8718716758293725 80.7344107943999
chr11 135006516 490110763 3.630274875028995 23.27119220171258
chr12 133851895 405591702 3.0301528566330718 4.399196762714992
chr13 115169878 338462032 2.938806898796923 3.0185450452164875
chr14 107349540 238771107 2.2242396846786674 19.355786078194367
chr15 102531392 282239353 2.752711608557894 3.5231480488238716
chr16 90354753 381792783 4.22548643345857 40.5240338799077
chr17 81195210 215770935 2.6574342870718604 11.863923592716848
chr18 78077248 419108930 5.367875286792895 45.3410403731464
chr19 59128983 216758396 3.665856996052173 54.988390100811365
chr20 63025520 203008915 3.2210589456461447 9.895841263656775
chr21 48129895 153235990 3.1838006295255785 14.272078027313619
chr22 51304566 113616347 2.2145464986488728 3.3685453693621503
chrMT 16571 2279132 137.53738458753244 30.272616147586792
chrX 155270560 706828559 4.552238099740221 15.817764212937085
chrY 59373566 34055661 0.5735828803006375 25.93711021441199