BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6234095.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 = 5,716,285
number of mapped reads = 5,410,265 (94.65%)
number of supplementary alignments = 39,016 (0.68%)
number of secondary alignments = 0
number of mapped bases = 350,831,469 bp
number of sequenced bases = 350,690,830 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 797,345
duplication rate = 12.1%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 42.7527
>>>>>>> ACTG content
number of A's = 89,742,788 bp (25.59%)
number of C's = 64,663,498 bp (18.44%)
number of T's = 112,475,437 bp (32.07%)
number of G's = 83,774,659 bp (23.89%)
number of N's = 34,448 bp (0.01%)
GC percentage = 42.33%
>>>>>>> Mismatches and indels
general error rate = 0.0055
number of mismatches = 1,877,036
number of insertions = 23,036
mapped reads with insertion percentage = 0.42%
number of deletions = 80,326
mapped reads with deletion percentage = 1.47%
homopolymer indels = 44.16%
>>>>>>> Coverage
mean coverageData = 0.1133X
std coverageData = 1.103X
There is a 7.69% of reference with a coverageData >= 1X
There is a 2.24% of reference with a coverageData >= 2X
There is a 0.72% of reference with a coverageData >= 3X
There is a 0.25% of reference with a coverageData >= 4X
There is a 0.1% of reference with a coverageData >= 5X
There is a 0.04% of reference with a coverageData >= 6X
There is a 0.02% of reference with a coverageData >= 7X
There is a 0.01% of reference with a coverageData >= 8X
There is a 0.01% of reference with a coverageData >= 9X
There is a 0.01% of reference with a coverageData >= 10X
There is a 0.01% of reference with a coverageData >= 11X
There is a 0.01% 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% 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 55341633 0.22203207670242875 1.7227019275162756
chr2 243199373 27899692 0.11471942405048881 2.1143119893646234
chr3 198022430 30710226 0.15508458309495546 0.5340124264504151
chr4 191154276 5240187 0.02741339147443398 0.37275962331026846
chr5 180915260 4898042 0.027073680793980565 0.2502309693547335
chr6 171115067 12243148 0.07154921080094016 0.5998142396645516
chr7 159138663 27041327 0.16992305006357883 2.0732453336553096
chr8 146364022 31312453 0.21393545061230962 1.3680713987112207
chr9 141213431 7691041 0.05446394826282494 0.5298211445574256
chr10 135534747 16778998 0.12379849722226581 0.8955396856202893
chr11 135006516 9137613 0.06768275540122819 0.591668892395335
chr12 133851895 17267878 0.12900734800952948 0.4926861845908699
chr13 115169878 22906097 0.19888965237941816 0.6622199766007576
chr14 107349540 18213312 0.1696636240825997 0.6120658159952493
chr15 102531392 3857129 0.03761900550418744 0.3273388615775507
chr16 90354753 8345009 0.09235827361511353 0.535758274245485
chr17 81195210 18322929 0.22566514699574028 0.7798471486860923
chr18 78077248 6589132 0.08439247243960238 1.7609544444761087
chr19 59128983 3302307 0.05584921019189523 1.0607219401351002
chr20 63025520 6771574 0.10744177913962472 0.5587808126161953
chr21 48129895 9173638 0.19060166243869844 0.6448507505204771
chr22 51304566 3422703 0.06671341884073242 0.34166797676459915
chrMT 16571 531572 32.07845030474926 19.106506368060867
chrX 155270560 3114145 0.020056248911577312 0.379602287880104
chrY 59373566 719684 0.012121286432416743 0.32005434854115206