BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR927021.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 31,605,058
number of mapped reads = 30,862,204 (97.65%)
number of supplementary alignments = 666,481 (2.11%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 15,440,746
number of mapped paired reads (second in pair) = 15,421,458
number of mapped paired reads (both in pair) = 30,417,402
number of mapped paired reads (singletons) = 444,802
number of mapped bases = 2,864,358,338 bp
number of sequenced bases = 2,862,167,517 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 2,597,485
duplication rate = 6.61%
>>>>>>> Insert size
mean insert size = 201,088.1557
std insert size = 4,456,256.8704
median insert size = 189
>>>>>>> Mapping quality
mean mapping quality = 52.9627
>>>>>>> ACTG content
number of A's = 810,022,051 bp (28.3%)
number of C's = 574,716,967 bp (20.08%)
number of T's = 822,719,574 bp (28.74%)
number of G's = 654,564,418 bp (22.87%)
number of N's = 144,507 bp (0.01%)
GC percentage = 42.95%
>>>>>>> Mismatches and indels
general error rate = 0.0096
number of mismatches = 26,510,668
number of insertions = 488,594
mapped reads with insertion percentage = 1.56%
number of deletions = 1,496,329
mapped reads with deletion percentage = 4.72%
homopolymer indels = 52.62%
>>>>>>> Coverage
mean coverageData = 0.9253X
std coverageData = 3.5624X
There is a 35.78% of reference with a coverageData >= 1X
There is a 20.34% of reference with a coverageData >= 2X
There is a 11.93% of reference with a coverageData >= 3X
There is a 7.44% of reference with a coverageData >= 4X
There is a 4.79% of reference with a coverageData >= 5X
There is a 3.18% of reference with a coverageData >= 6X
There is a 2.15% of reference with a coverageData >= 7X
There is a 1.49% of reference with a coverageData >= 8X
There is a 1.05% of reference with a coverageData >= 9X
There is a 0.75% of reference with a coverageData >= 10X
There is a 0.54% of reference with a coverageData >= 11X
There is a 0.4% of reference with a coverageData >= 12X
There is a 0.29% of reference with a coverageData >= 13X
There is a 0.22% of reference with a coverageData >= 14X
There is a 0.17% of reference with a coverageData >= 15X
There is a 0.13% of reference with a coverageData >= 16X
There is a 0.1% of reference with a coverageData >= 17X
There is a 0.08% of reference with a coverageData >= 18X
There is a 0.06% of reference with a coverageData >= 19X
There is a 0.05% of reference with a coverageData >= 20X
There is a 0.04% of reference with a coverageData >= 21X
There is a 0.04% of reference with a coverageData >= 22X
There is a 0.03% of reference with a coverageData >= 23X
There is a 0.03% of reference with a coverageData >= 24X
There is a 0.02% of reference with a coverageData >= 25X
There is a 0.02% of reference with a coverageData >= 26X
There is a 0.02% of reference with a coverageData >= 27X
There is a 0.02% of reference with a coverageData >= 28X
There is a 0.01% of reference with a coverageData >= 29X
There is a 0.01% of reference with a coverageData >= 30X
There is a 0.01% of reference with a coverageData >= 31X
There is a 0.01% of reference with a coverageData >= 32X
There is a 0.01% of reference with a coverageData >= 33X
There is a 0.01% of reference with a coverageData >= 34X
There is a 0.01% of reference with a coverageData >= 35X
There is a 0.01% of reference with a coverageData >= 36X
There is a 0.01% of reference with a coverageData >= 37X
There is a 0.01% of reference with a coverageData >= 38X
There is a 0.01% of reference with a coverageData >= 39X
There is a 0.01% of reference with a coverageData >= 40X
There is a 0.01% of reference with a coverageData >= 41X
There is a 0.01% of reference with a coverageData >= 42X
There is a 0.01% of reference with a coverageData >= 43X
There is a 0.01% of reference with a coverageData >= 44X
There is a 0.01% of reference with a coverageData >= 45X
There is a 0.01% of reference with a coverageData >= 46X
There is a 0.01% 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 244409775 0.9805783994415805 4.56809811083922
chr2 243199373 239197840 0.9835462857052678 5.335154641849336
chr3 198022430 187548441 0.9471070575186862 1.893240005178291
chr4 191154276 157474074 0.8238061805114942 2.5082536072164334
chr5 180915260 161413991 0.8922077164745528 1.7693371128938775
chr6 171115067 153885923 0.8993125251793286 1.8556823654588859
chr7 159138663 145866252 0.9165984509999308 2.516783244559912
chr8 146364022 133541271 0.9123913730657115 2.0110492545482033
chr9 141213431 119749224 0.8480016606918926 3.5689081380657353
chr10 135534747 145011882 1.069924024722605 7.930521832362154
chr11 135006516 138540308 1.0261749736583086 3.5872605036966485
chr12 133851895 127840421 0.9550886149202445 1.9657169462904505
chr13 115169878 77277333 0.6709856287248998 1.5271431017822128
chr14 107349540 93413237 0.8701782699767507 1.8977875964638393
chr15 102531392 88249493 0.8607070603313374 1.8714703850048777
chr16 90354753 100294194 1.1100046280907878 4.679253081161668
chr17 81195210 88986829 1.0959615598013726 2.3610894355248417
chr18 78077248 77726581 0.9955087172129837 3.802200349211516
chr19 59128983 62517945 1.057314735144354 3.0777491490708058
chr20 63025520 74862095 1.187806066494969 2.3120006402493933
chr21 48129895 38811017 0.8063806704751797 2.7187792838143334
chr22 51304566 48437423 0.9441152469743141 2.1558533802663056
chrMT 16571 5367170 323.88932472391525 246.13694848701036
chrX 155270560 148597885 0.9570254979437184 2.14998829924286
chrY 59373566 5337734 0.08990084914219233 2.3717274081305084