BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6234132.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 = 1,778,767
number of mapped reads = 985,582 (55.41%)
number of supplementary alignments = 10,993 (0.62%)
number of secondary alignments = 0
number of mapped bases = 61,530,466 bp
number of sequenced bases = 61,486,679 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 99,217
duplication rate = 8.49%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.9436
>>>>>>> ACTG content
number of A's = 16,547,186 bp (26.91%)
number of C's = 10,823,525 bp (17.6%)
number of T's = 20,104,764 bp (32.7%)
number of G's = 14,000,600 bp (22.77%)
number of N's = 10,604 bp (0.02%)
GC percentage = 40.37%
>>>>>>> Mismatches and indels
general error rate = 0.0094
number of mismatches = 563,507
number of insertions = 5,439
mapped reads with insertion percentage = 0.54%
number of deletions = 25,299
mapped reads with deletion percentage = 2.53%
homopolymer indels = 44.24%
>>>>>>> Coverage
mean coverageData = 0.0199X
std coverageData = 0.2339X
There is a 1.39% of reference with a coverageData >= 1X
There is a 0.39% of reference with a coverageData >= 2X
There is a 0.12% of reference with a coverageData >= 3X
There is a 0.04% 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 5864247 0.023527512093941785 0.33341117888763655
chr2 243199373 4469723 0.01837884261321677 0.28226271227797967
chr3 198022430 4126375 0.020837917199581887 0.1961643797502406
chr4 191154276 1874356 0.009805462055162188 0.1517818292292776
chr5 180915260 4625531 0.02556738994820006 0.21812922048711664
chr6 171115067 5338682 0.031199368317460906 0.26893694100514104
chr7 159138663 2894010 0.018185461316839138 0.2050579607051441
chr8 146364022 2985811 0.020399897182382703 0.2849470729051034
chr9 141213431 3572652 0.02529966147483521 0.24121585957516176
chr10 135534747 2790890 0.020591693730021867 0.23652969836051932
chr11 135006516 2815327 0.02085326755636002 0.2184993886957048
chr12 133851895 1895402 0.014160442031844226 0.16229792165546628
chr13 115169878 3447875 0.029937298361990102 0.24637977755814122
chr14 107349540 3454249 0.0321775854838316 0.2544902480605752
chr15 102531392 1166569 0.011377676409581955 0.1463061195780677
chr16 90354753 1145798 0.012681103782110943 0.17354601912341563
chr17 81195210 976670 0.012028665237764642 0.15357453538854113
chr18 78077248 1408851 0.018044321951511406 0.34439502987793563
chr19 59128983 833555 0.014097232147557823 0.2164286704470939
chr20 63025520 929635 0.014750136135330577 0.17584605756868024
chr21 48129895 1043367 0.021678148269386417 0.2091574482332538
chr22 51304566 331557 0.006462524212757204 0.10479081210774734
chrMT 16571 41501 2.5044354595377465 2.771449938771103
chrX 155270560 3292718 0.02120632526861499 0.20428136838219824
chrY 59373566 205115 0.003454651856349676 0.10186743656596775