BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3472701.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 12,739,244
number of mapped reads = 12,640,322 (99.22%)
number of supplementary alignments = 44,670 (0.35%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 6,338,113
number of mapped paired reads (second in pair) = 6,302,209
number of mapped paired reads (both in pair) = 12,580,130
number of mapped paired reads (singletons) = 60,192
number of mapped bases = 1,243,026,774 bp
number of sequenced bases = 1,242,866,727 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 7,688,515
duplication rate = 45.59%
>>>>>>> Insert size
mean insert size = 23,770.3482
std insert size = 1,515,830.2241
median insert size = 227
>>>>>>> Mapping quality
mean mapping quality = 55.086
>>>>>>> ACTG content
number of A's = 334,509,271 bp (26.91%)
number of C's = 289,030,937 bp (23.26%)
number of T's = 332,391,078 bp (26.74%)
number of G's = 286,694,043 bp (23.07%)
number of N's = 241,398 bp (0.02%)
GC percentage = 46.32%
>>>>>>> Mismatches and indels
general error rate = 0.0059
number of mismatches = 7,209,562
number of insertions = 69,556
mapped reads with insertion percentage = 0.55%
number of deletions = 66,137
mapped reads with deletion percentage = 0.52%
homopolymer indels = 44.45%
>>>>>>> Coverage
mean coverageData = 0.4015X
std coverageData = 16.0048X
There is a 3.81% of reference with a coverageData >= 1X
There is a 1.7% of reference with a coverageData >= 2X
There is a 0.76% of reference with a coverageData >= 3X
There is a 0.56% of reference with a coverageData >= 4X
There is a 0.43% of reference with a coverageData >= 5X
There is a 0.38% of reference with a coverageData >= 6X
There is a 0.35% of reference with a coverageData >= 7X
There is a 0.32% of reference with a coverageData >= 8X
There is a 0.31% of reference with a coverageData >= 9X
There is a 0.29% of reference with a coverageData >= 10X
There is a 0.28% of reference with a coverageData >= 11X
There is a 0.27% of reference with a coverageData >= 12X
There is a 0.26% of reference with a coverageData >= 13X
There is a 0.25% of reference with a coverageData >= 14X
There is a 0.25% of reference with a coverageData >= 15X
There is a 0.24% of reference with a coverageData >= 16X
There is a 0.23% of reference with a coverageData >= 17X
There is a 0.23% of reference with a coverageData >= 18X
There is a 0.22% of reference with a coverageData >= 19X
There is a 0.22% of reference with a coverageData >= 20X
There is a 0.21% of reference with a coverageData >= 21X
There is a 0.21% of reference with a coverageData >= 22X
There is a 0.2% of reference with a coverageData >= 23X
There is a 0.2% of reference with a coverageData >= 24X
There is a 0.19% of reference with a coverageData >= 25X
There is a 0.19% of reference with a coverageData >= 26X
There is a 0.19% of reference with a coverageData >= 27X
There is a 0.18% of reference with a coverageData >= 28X
There is a 0.18% of reference with a coverageData >= 29X
There is a 0.18% of reference with a coverageData >= 30X
There is a 0.17% of reference with a coverageData >= 31X
There is a 0.17% of reference with a coverageData >= 32X
There is a 0.17% of reference with a coverageData >= 33X
There is a 0.16% of reference with a coverageData >= 34X
There is a 0.16% of reference with a coverageData >= 35X
There is a 0.16% of reference with a coverageData >= 36X
There is a 0.16% of reference with a coverageData >= 37X
There is a 0.15% of reference with a coverageData >= 38X
There is a 0.15% of reference with a coverageData >= 39X
There is a 0.15% of reference with a coverageData >= 40X
There is a 0.15% of reference with a coverageData >= 41X
There is a 0.14% of reference with a coverageData >= 42X
There is a 0.14% of reference with a coverageData >= 43X
There is a 0.14% of reference with a coverageData >= 44X
There is a 0.14% of reference with a coverageData >= 45X
There is a 0.14% of reference with a coverageData >= 46X
There is a 0.14% of reference with a coverageData >= 47X
There is a 0.13% of reference with a coverageData >= 48X
There is a 0.13% of reference with a coverageData >= 49X
There is a 0.13% of reference with a coverageData >= 50X
There is a 0.13% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 141651356 0.5683089391380092 23.486702897633762
chr2 243199373 104124059 0.42814279377274544 16.400439535670262
chr3 198022430 133954595 0.676461727088189 15.848219109365989
chr4 191154276 36281225 0.18980075025891652 6.878362579970984
chr5 180915260 61842194 0.3418296168051274 11.61302703735752
chr6 171115067 60206005 0.35184514172559683 9.345047535391362
chr7 159138663 41888971 0.26322309242977615 8.411843785950234
chr8 146364022 51688587 0.3531509061700969 10.649370900999173
chr9 141213431 61585350 0.43611538621988444 11.848749669759762
chr10 135534747 30885342 0.22787766741468887 8.921989840049122
chr11 135006516 60458738 0.44782088888213367 15.5313285865584
chr12 133851895 58252421 0.43520057000313667 19.333309974890792
chr13 115169878 37523009 0.32580575452202876 14.341910795908355
chr14 107349540 29612071 0.2758472090332199 11.200882929516965
chr15 102531392 22797866 0.2223501071749811 6.828930959893134
chr16 90354753 48589435 0.5377629110446465 14.95156597715051
chr17 81195210 46519727 0.5729368395007538 14.63832496360919
chr18 78077248 30294395 0.38800541484249035 14.996140503580332
chr19 59128983 31020338 0.5246215379689517 13.772760203290337
chr20 63025520 71514016 1.134683474249796 57.373166074321325
chr21 48129895 3395322 0.0705449700233088 2.596605337624347
chr22 51304566 13269440 0.2586405272388426 8.524214792701432
chrMT 16571 1253 0.07561402450063363 0.3059767972503758
chrX 155270560 65425592 0.4213650804118952 14.11661135063543
chrY 59373566 245467 0.004134280902043175 0.26436619192327004