BamQC report
-----------------------------------
>>>>>>> Input
bam file = ERR2094003.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 365,900
number of mapped reads = 150,403 (41.1%)
number of supplementary alignments = 900 (0.25%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 74,608
number of mapped paired reads (second in pair) = 75,795
number of mapped paired reads (both in pair) = 147,288
number of mapped paired reads (singletons) = 3,115
number of mapped bases = 21,415,838 bp
number of sequenced bases = 21,238,911 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 147,108
duplication rate = 31.16%
>>>>>>> Insert size
mean insert size = 36,971.6572
std insert size = 2,010,457.9009
median insert size = 217
>>>>>>> Mapping quality
mean mapping quality = 24.9596
>>>>>>> ACTG content
number of A's = 6,190,469 bp (29.15%)
number of C's = 4,190,820 bp (19.73%)
number of T's = 6,252,478 bp (29.44%)
number of G's = 4,604,860 bp (21.68%)
number of N's = 284 bp (0%)
GC percentage = 41.41%
>>>>>>> Mismatches and indels
general error rate = 0.0238
number of mismatches = 500,683
number of insertions = 3,775
mapped reads with insertion percentage = 2.4%
number of deletions = 21,692
mapped reads with deletion percentage = 14.12%
homopolymer indels = 41.49%
>>>>>>> Coverage
mean coverageData = 0.0069X
std coverageData = 14.8191X
There is a 0.01% of reference with a coverageData >= 1X
There is a 0% of reference with a coverageData >= 2X
There is a 0% of reference with a coverageData >= 3X
There is a 0% of reference with a coverageData >= 4X
There is a 0% of reference with a coverageData >= 5X
There is a 0% of reference with a coverageData >= 6X
There is a 0% of reference with a coverageData >= 7X
There is a 0% of reference with a coverageData >= 8X
There is a 0% of reference with a coverageData >= 9X
There is a 0% of reference with a coverageData >= 10X
There is a 0% of reference with a coverageData >= 11X
There is a 0% of reference with a coverageData >= 12X
There is a 0% of reference with a coverageData >= 13X
There is a 0% of reference with a coverageData >= 14X
There is a 0% of reference with a coverageData >= 15X
There is a 0% of reference with a coverageData >= 16X
There is a 0% of reference with a coverageData >= 17X
There is a 0% of reference with a coverageData >= 18X
There is a 0% of reference with a coverageData >= 19X
There is a 0% of reference with a coverageData >= 20X
There is a 0% of reference with a coverageData >= 21X
There is a 0% 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 14794 5.935391430780026E-5 0.013859882356400427
chr2 243199373 264409 0.0010872108621760304 0.9302098813281957
chr3 198022430 227743 0.0011500868866218842 1.025892598129064
chr4 191154276 765257 0.0040033475369392205 4.368175109147787
chr5 180915260 16005 8.84668324827878E-5 0.03451595411114171
chr6 171115067 15793 9.229461950302716E-5 0.04250322817202771
chr7 159138663 12029 7.55881680368271E-5 0.017402759546916932
chr8 146364022 16766 1.1455000874463534E-4 0.03545463880777814
chr9 141213431 6804 4.818238571088893E-5 0.010412259189757597
chr10 135534747 7520 5.5483926937200835E-5 0.013553559610618618
chr11 135006516 60201 4.4591181065660565E-4 0.3098052257764189
chr12 133851895 94577 7.065794623228905E-4 0.44001880823360306
chr13 115169878 16863 1.4641849321052507E-4 0.07034522977800563
chr14 107349540 50164 4.6729590084876007E-4 0.31367546276863795
chr15 102531392 7946 7.749821635114443E-5 0.031241116056521894
chr16 90354753 3242 3.588079090869741E-5 0.007900590855414885
chr17 81195210 7271 8.954961752054093E-5 0.02149337443943128
chr18 78077248 3672 4.7030346151544686E-5 0.011873770936656416
chr19 59128983 99758 0.0016871252461758053 0.999374085080185
chr20 63025520 3766 5.9753572838431165E-5 0.010114554654055323
chr21 48129895 4950 1.0284668188035731E-4 0.016275673599034608
chr22 51304566 2871 5.595993151954545E-5 0.012002421433455273
chrMT 16571 17075227 1030.4282783175427 6240.508842218057
chrX 155270560 2630527 0.01694156960598326 9.0550961310697
chrY 59373566 7683 1.2940101997579193E-4 0.03878950981824608