BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR617490.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000
number of mapped reads = 30,245,925 (94.52%)
number of supplementary alignments = 162,815 (0.51%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 15,235,160
number of mapped paired reads (second in pair) = 15,010,765
number of mapped paired reads (both in pair) = 29,688,690
number of mapped paired reads (singletons) = 557,235
number of mapped bases = 2,938,464,701 bp
number of sequenced bases = 2,936,724,864 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 6,187,213
duplication rate = 9.9%
>>>>>>> Insert size
mean insert size = 41,515.5721
std insert size = 1,916,405.4727
median insert size = 220
>>>>>>> Mapping quality
mean mapping quality = 52.6648
>>>>>>> ACTG content
number of A's = 866,347,201 bp (29.5%)
number of C's = 592,732,992 bp (20.18%)
number of T's = 866,024,323 bp (29.49%)
number of G's = 607,712,189 bp (20.69%)
number of N's = 3,908,159 bp (0.13%)
GC percentage = 40.88%
>>>>>>> Mismatches and indels
general error rate = 0.0129
number of mismatches = 37,080,553
number of insertions = 440,337
mapped reads with insertion percentage = 1.43%
number of deletions = 1,020,807
mapped reads with deletion percentage = 3.31%
homopolymer indels = 47.44%
>>>>>>> Coverage
mean coverageData = 0.9492X
std coverageData = 9.5122X
There is a 38.02% of reference with a coverageData >= 1X
There is a 20.43% of reference with a coverageData >= 2X
There is a 11.49% of reference with a coverageData >= 3X
There is a 6.81% of reference with a coverageData >= 4X
There is a 4.19% of reference with a coverageData >= 5X
There is a 2.68% of reference with a coverageData >= 6X
There is a 1.77% of reference with a coverageData >= 7X
There is a 1.2% of reference with a coverageData >= 8X
There is a 0.84% of reference with a coverageData >= 9X
There is a 0.61% of reference with a coverageData >= 10X
There is a 0.45% of reference with a coverageData >= 11X
There is a 0.34% of reference with a coverageData >= 12X
There is a 0.26% of reference with a coverageData >= 13X
There is a 0.21% of reference with a coverageData >= 14X
There is a 0.17% of reference with a coverageData >= 15X
There is a 0.14% of reference with a coverageData >= 16X
There is a 0.11% of reference with a coverageData >= 17X
There is a 0.1% of reference with a coverageData >= 18X
There is a 0.08% of reference with a coverageData >= 19X
There is a 0.07% of reference with a coverageData >= 20X
There is a 0.06% of reference with a coverageData >= 21X
There is a 0.06% of reference with a coverageData >= 22X
There is a 0.05% of reference with a coverageData >= 23X
There is a 0.05% of reference with a coverageData >= 24X
There is a 0.04% of reference with a coverageData >= 25X
There is a 0.04% of reference with a coverageData >= 26X
There is a 0.04% of reference with a coverageData >= 27X
There is a 0.03% of reference with a coverageData >= 28X
There is a 0.03% of reference with a coverageData >= 29X
There is a 0.03% of reference with a coverageData >= 30X
There is a 0.03% of reference with a coverageData >= 31X
There is a 0.03% of reference with a coverageData >= 32X
There is a 0.02% of reference with a coverageData >= 33X
There is a 0.02% of reference with a coverageData >= 34X
There is a 0.02% of reference with a coverageData >= 35X
There is a 0.02% of reference with a coverageData >= 36X
There is a 0.02% of reference with a coverageData >= 37X
There is a 0.02% of reference with a coverageData >= 38X
There is a 0.02% of reference with a coverageData >= 39X
There is a 0.02% of reference with a coverageData >= 40X
There is a 0.02% of reference with a coverageData >= 41X
There is a 0.02% of reference with a coverageData >= 42X
There is a 0.02% of reference with a coverageData >= 43X
There is a 0.02% of reference with a coverageData >= 44X
There is a 0.02% of reference with a coverageData >= 45X
There is a 0.02% of reference with a coverageData >= 46X
There is a 0.02% of reference with a coverageData >= 47X
There is a 0.01% of reference with a coverageData >= 48X
There is a 0.01% of reference with a coverageData >= 49X
There is a 0.01% of reference with a coverageData >= 50X
There is a 0.01% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 189676296 0.7609862524675515 9.29843171702736
chr2 243199373 303783444 1.249112776289929 11.272677433333033
chr3 198022430 242776116 1.2260031148996606 2.2321900726144706
chr4 191154276 151489773 0.7925000484948608 5.929150035432976
chr5 180915260 188075135 1.0395758489361262 2.0702807918517045
chr6 171115067 138274983 0.808081868091721 5.330496530936884
chr7 159138663 226582135 1.4238031835167548 12.921332717501471
chr8 146364022 130440506 0.8912060779526816 3.778600888861215
chr9 141213431 121841688 0.8628194013641662 17.839830936689804
chr10 135534747 124521488 0.9187421731786609 18.255402361160353
chr11 135006516 165671765 1.227139029348776 12.432428743919258
chr12 133851895 128446279 0.9596149460566098 2.028597581484505
chr13 115169878 124842565 1.0839862572399357 2.1288625736195623
chr14 107349540 85451804 0.7960146266113484 2.176999485800648
chr15 102531392 66463224 0.6482231705193274 1.558449523211834
chr16 90354753 79272542 0.8773477804759203 14.604535658215076
chr17 81195210 82032436 1.0103112732881656 13.422116016913897
chr18 78077248 52669922 0.6745873266434801 16.812360941567434
chr19 59128983 34915473 0.590496761968661 5.602130464719614
chr20 63025520 86844087 1.3779194047109806 2.795542074877634
chr21 48129895 42361968 0.8801591609539144 3.7343399727786073
chr22 51304566 21958450 0.4280018663446057 1.2421894489512433
chrMT 16571 2062491 124.4638826866212 93.04335852226868
chrX 155270560 137907515 0.8881755498273466 4.083012556492336
chrY 59373566 10102616 0.1701534315792991 13.357461912817152