BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3084850.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,831,495
number of mapped reads = 2,516,653 (88.88%)
number of supplementary alignments = 21,277 (0.75%)
number of secondary alignments = 0
number of mapped bases = 174,219,547 bp
number of sequenced bases = 174,152,043 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 143,550
duplication rate = 4.79%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 48.2037
>>>>>>> ACTG content
number of A's = 50,695,541 bp (29.11%)
number of C's = 31,755,714 bp (18.23%)
number of T's = 56,153,262 bp (32.24%)
number of G's = 35,520,041 bp (20.4%)
number of N's = 27,485 bp (0.02%)
GC percentage = 38.63%
>>>>>>> Mismatches and indels
general error rate = 0.0084
number of mismatches = 1,433,505
number of insertions = 14,060
mapped reads with insertion percentage = 0.55%
number of deletions = 37,939
mapped reads with deletion percentage = 1.49%
homopolymer indels = 48.63%
>>>>>>> Coverage
mean coverageData = 0.0563X
std coverageData = 0.461X
There is a 4.39% of reference with a coverageData >= 1X
There is a 0.91% of reference with a coverageData >= 2X
There is a 0.2% of reference with a coverageData >= 3X
There is a 0.05% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0.01% 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 13185286 0.052899711732313 0.6882096380228597
chr2 243199373 15307956 0.06294406030397126 0.41939914909401194
chr3 198022430 11986553 0.06053128930899394 0.30144618534684275
chr4 191154276 12100847 0.06330408742726738 0.31748575609156926
chr5 180915260 11474269 0.06342344476635083 0.3095960721034564
chr6 171115067 10541062 0.061602184920396284 0.30707756748676857
chr7 159138663 9295235 0.058409658751500254 0.3455477463140559
chr8 146364022 9002808 0.06150970625827705 1.1825397795218984
chr9 141213431 7096841 0.05025613321441075 0.4019476066078078
chr10 135534747 7977047 0.058856102782262915 0.37476287707035055
chr11 135006516 8422836 0.06238836649928808 0.39164354622255704
chr12 133851895 8175659 0.061079889828978516 0.3055925283456886
chr13 115169878 5935392 0.051535975404957884 0.27692348356914415
chr14 107349540 5219453 0.04862110261487846 0.2857871241587318
chr15 102531392 4888905 0.04768203088474601 0.26456019725614827
chr16 90354753 4335366 0.04798160424388521 0.288124245784147
chr17 81195210 3822617 0.04707934125670714 0.29357678700453044
chr18 78077248 4950093 0.06339994206763025 0.7380788086244642
chr19 59128983 2506220 0.042385643602224646 0.4766630192124239
chr20 63025520 3182484 0.05049516449844444 0.2842165087457551
chr21 48129895 2273062 0.04722765341582399 0.2803523826213062
chr22 51304566 1609744 0.031376232672935975 0.21094428922804034
chrMT 16571 117328 7.080321042785589 4.626651135816785
chrX 155270560 10423715 0.06713259100759346 0.3423603239654544
chrY 59373566 388769 0.0065478465618858065 0.15880693733607043