BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR536741.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP014781/SRP014781.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 = 86,574,968
number of mapped reads = 83,179,987 (96.08%)
number of supplementary alignments = 1,684 (0%)
number of secondary alignments = 0
number of mapped bases = 4,144,627,242 bp
number of sequenced bases = 4,144,243,991 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 4,997,824
duplication rate = 2.4%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.1556
>>>>>>> ACTG content
number of A's = 1,210,731,665 bp (29.21%)
number of C's = 858,040,524 bp (20.7%)
number of T's = 1,215,031,569 bp (29.32%)
number of G's = 860,333,109 bp (20.76%)
number of N's = 107,124 bp (0%)
GC percentage = 41.46%
>>>>>>> Mismatches and indels
general error rate = 0.0025
number of mismatches = 10,083,698
number of insertions = 158,863
mapped reads with insertion percentage = 0.19%
number of deletions = 228,080
mapped reads with deletion percentage = 0.27%
homopolymer indels = 44.41%
>>>>>>> Coverage
mean coverageData = 1.3388X
std coverageData = 10.9681X
There is a 67.57% of reference with a coverageData >= 1X
There is a 36.61% of reference with a coverageData >= 2X
There is a 15.59% of reference with a coverageData >= 3X
There is a 5.53% of reference with a coverageData >= 4X
There is a 1.75% of reference with a coverageData >= 5X
There is a 0.55% of reference with a coverageData >= 6X
There is a 0.21% of reference with a coverageData >= 7X
There is a 0.12% of reference with a coverageData >= 8X
There is a 0.09% of reference with a coverageData >= 9X
There is a 0.07% of reference with a coverageData >= 10X
There is a 0.06% of reference with a coverageData >= 11X
There is a 0.05% of reference with a coverageData >= 12X
There is a 0.05% of reference with a coverageData >= 13X
There is a 0.04% of reference with a coverageData >= 14X
There is a 0.04% of reference with a coverageData >= 15X
There is a 0.04% of reference with a coverageData >= 16X
There is a 0.03% of reference with a coverageData >= 17X
There is a 0.03% of reference with a coverageData >= 18X
There is a 0.03% of reference with a coverageData >= 19X
There is a 0.03% of reference with a coverageData >= 20X
There is a 0.03% of reference with a coverageData >= 21X
There is a 0.03% 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 0.02% of reference with a coverageData >= 29X
There is a 0.02% of reference with a coverageData >= 30X
There is a 0.02% of reference with a coverageData >= 31X
There is a 0.02% 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 0.02% of reference with a coverageData >= 48X
There is a 0.02% of reference with a coverageData >= 49X
There is a 0.02% of reference with a coverageData >= 50X
There is a 0.02% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 342640204 1.3746814456281735 22.85509385797162
chr2 243199373 348667065 1.4336676147598457 5.703279561332136
chr3 198022430 275949263 1.3935252839791936 3.1730497630085455
chr4 191154276 267382167 1.3987768026701113 3.5677493342427025
chr5 180915260 252987766 1.3983771518223505 2.6442247304212825
chr6 171115067 240613312 1.4061491849808878 7.064097636950038
chr7 159138663 228436767 1.4354573721660586 10.09265629147275
chr8 146364022 208092052 1.4217431931461955 5.454409134265298
chr9 141213431 174417433 1.2351334555421998 4.402348790782014
chr10 135534747 212831688 1.5703108812384472 20.418822709165955
chr11 135006516 191796354 1.4206451635267738 5.267549027700157
chr12 133851895 186050027 1.3899693164598081 2.1871566008412624
chr13 115169878 131304298 1.1400923599137616 1.7477870289590227
chr14 107349540 125891416 1.17272431721645 2.0993051237435822
chr15 102531392 119399854 1.1645199745264359 1.380846186584215
chr16 90354753 131285321 1.45299850468298 8.917102443979422
chr17 81195210 115965731 1.4282336482657043 3.1433333936146153
chr18 78077248 109488231 1.4023064824211018 10.815294001153191
chr19 59128983 87359761 1.477443997303319 16.842842876187223
chr20 63025520 88371812 1.4021591888492153 2.118150254561016
chr21 48129895 56031648 1.164175571128921 4.570477847200594
chr22 51304566 51989216 1.0133448161319598 3.754536826172093
chrMT 16571 37962221 2290.882928006759 615.7198519971747
chrX 155270560 118550529 0.7635093800138287 2.8463948153392824
chrY 59373566 41163106 0.6932901082613094 8.642302903957331