BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6068060.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 = 1,888,412
number of mapped reads = 1,516,350 (80.3%)
number of supplementary alignments = 13,638 (0.72%)
number of secondary alignments = 0
number of mapped bases = 98,733,992 bp
number of sequenced bases = 98,696,973 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 307,572
duplication rate = 13.52%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.0323
>>>>>>> ACTG content
number of A's = 26,691,852 bp (27.04%)
number of C's = 17,431,508 bp (17.66%)
number of T's = 32,124,670 bp (32.55%)
number of G's = 22,348,936 bp (22.64%)
number of N's = 100,007 bp (0.1%)
GC percentage = 40.31%
>>>>>>> Mismatches and indels
general error rate = 0.0087
number of mismatches = 842,321
number of insertions = 7,934
mapped reads with insertion percentage = 0.52%
number of deletions = 22,753
mapped reads with deletion percentage = 1.48%
homopolymer indels = 47.9%
>>>>>>> Coverage
mean coverageData = 0.0319X
std coverageData = 0.4652X
There is a 1.23% of reference with a coverageData >= 1X
There is a 0.64% of reference with a coverageData >= 2X
There is a 0.41% of reference with a coverageData >= 3X
There is a 0.27% of reference with a coverageData >= 4X
There is a 0.18% of reference with a coverageData >= 5X
There is a 0.12% of reference with a coverageData >= 6X
There is a 0.08% of reference with a coverageData >= 7X
There is a 0.06% of reference with a coverageData >= 8X
There is a 0.04% of reference with a coverageData >= 9X
There is a 0.03% of reference with a coverageData >= 10X
There is a 0.02% of reference with a coverageData >= 11X
There is a 0.02% of reference with a coverageData >= 12X
There is a 0.01% of reference with a coverageData >= 13X
There is a 0.01% of reference with a coverageData >= 14X
There is a 0.01% of reference with a coverageData >= 15X
There is a 0.01% 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 8769268 0.035182532203199605 0.7058825709223777
chr2 243199373 7563031 0.031098069483920916 0.5128304556219536
chr3 198022430 6332036 0.03197635742577242 0.4035344287235422
chr4 191154276 6841410 0.035789991953933585 0.4298992653857008
chr5 180915260 5717234 0.031601723370377935 0.39457690358032194
chr6 171115067 5589920 0.032667608399440363 0.42764195071032296
chr7 159138663 6147986 0.038632887094194074 0.565890386084241
chr8 146364022 4710252 0.03218176117078827 0.4531901328712789
chr9 141213431 4825406 0.03417101309577274 0.45688676076967205
chr10 135534747 4819629 0.0355600988431402 0.49751374931094194
chr11 135006516 4170564 0.030891575633282767 0.4205352494652824
chr12 133851895 4021035 0.03004092695138907 0.3796052917349037
chr13 115169878 3443720 0.02990122122036111 0.39190785461482053
chr14 107349540 2850226 0.02655089160139857 0.375327050735934
chr15 102531392 2511314 0.024493123042745778 0.342464203181626
chr16 90354753 3006793 0.033277640635020055 0.4049951417129416
chr17 81195210 2285451 0.028147608707459467 0.37440088668424415
chr18 78077248 2584346 0.033099860281960755 0.6007148757264309
chr19 59128983 1923618 0.0325325737464485 0.49026569100954115
chr20 63025520 1800549 0.028568570318816884 0.3697877874872465
chr21 48129895 1211007 0.025161222562401185 0.34882529640083876
chr22 51304566 929549 0.018118250917471945 0.2793522559671528
chrMT 16571 80376 4.850401303481987 4.814841843415577
chrX 155270560 6293563 0.040532880154486466 0.4636716134003863
chrY 59373566 305709 0.005148907512141009 0.1574246757737146