BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6008804.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,923,991
number of mapped reads = 1,706,348 (88.69%)
number of supplementary alignments = 12,429 (0.65%)
number of secondary alignments = 0
number of mapped bases = 113,094,421 bp
number of sequenced bases = 113,035,987 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 74,753
duplication rate = 3.26%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.9303
>>>>>>> ACTG content
number of A's = 30,691,906 bp (27.15%)
number of C's = 21,879,336 bp (19.36%)
number of T's = 34,754,467 bp (30.75%)
number of G's = 25,566,460 bp (22.62%)
number of N's = 143,818 bp (0.13%)
GC percentage = 41.97%
>>>>>>> Mismatches and indels
general error rate = 0.0085
number of mismatches = 948,155
number of insertions = 7,881
mapped reads with insertion percentage = 0.46%
number of deletions = 33,130
mapped reads with deletion percentage = 1.92%
homopolymer indels = 45.41%
>>>>>>> Coverage
mean coverageData = 0.0365X
std coverageData = 0.378X
There is a 3% of reference with a coverageData >= 1X
There is a 0.46% of reference with a coverageData >= 2X
There is a 0.08% of reference with a coverageData >= 3X
There is a 0.02% of reference with a coverageData >= 4X
There is a 0.01% 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 12193956 0.04892246988624353 0.7207521650250013
chr2 243199373 8487504 0.034899366290718194 0.40050468678641704
chr3 198022430 10089912 0.05095337937222566 0.2935664534418722
chr4 191154276 7474240 0.039100563986337405 0.23782484470287898
chr5 180915260 4519627 0.024982010914944376 0.1844495752833199
chr6 171115067 6977557 0.04077698780318392 0.2799598193352659
chr7 159138663 5349257 0.03361381137153326 0.49339695140060347
chr8 146364022 9056573 0.061877043799739254 0.4465903079549981
chr9 141213431 3285513 0.023266292566746005 0.2552806909680693
chr10 135534747 8323627 0.0614132330213447 0.6944499938628533
chr11 135006516 4392348 0.03253434078692913 0.26266556755070514
chr12 133851895 4444313 0.03320321314838314 0.2138681185009266
chr13 115169878 1669130 0.01449276520028961 0.13941788070589722
chr14 107349540 3403898 0.0317085476099851 0.2133996217686615
chr15 102531392 2368507 0.023100310585854527 0.17676026591329397
chr16 90354753 2636043 0.029174370052231783 0.2670305277390699
chr17 81195210 3938936 0.048511925765079 0.3040587730168877
chr18 78077248 1713997 0.021952579578624492 0.394424143931835
chr19 59128983 3138517 0.05307916423998025 0.5171413704945979
chr20 63025520 2876060 0.04563326093937821 0.2527840538447127
chr21 48129895 1340128 0.02784398345352717 0.2066007099621013
chr22 51304566 1882235 0.03668747534088876 0.2242390745742227
chrMT 16571 56837 3.429907670025949 3.0196978490199795
chrX 155270560 3217863 0.020724231303087978 0.1818305008129736
chrY 59373566 257843 0.004342723831005872 0.15707945556272054