BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6231779.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 = 1,152,148
number of mapped reads = 1,005,448 (87.27%)
number of supplementary alignments = 7,498 (0.65%)
number of secondary alignments = 0
number of mapped bases = 66,177,523 bp
number of sequenced bases = 66,151,245 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 67,741
duplication rate = 1.99%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.1779
>>>>>>> ACTG content
number of A's = 19,294,709 bp (29.17%)
number of C's = 12,352,060 bp (18.67%)
number of T's = 18,119,793 bp (27.39%)
number of G's = 16,380,145 bp (24.76%)
number of N's = 4,538 bp (0.01%)
GC percentage = 43.43%
>>>>>>> Mismatches and indels
general error rate = 0.0074
number of mismatches = 478,455
number of insertions = 5,965
mapped reads with insertion percentage = 0.58%
number of deletions = 15,581
mapped reads with deletion percentage = 1.53%
homopolymer indels = 42.34%
>>>>>>> Coverage
mean coverageData = 0.0214X
std coverageData = 5.289X
There is a 1.89% of reference with a coverageData >= 1X
There is a 0.09% of reference with a coverageData >= 2X
There is a 0.01% of reference with a coverageData >= 3X
There is a 0% of reference with a coverageData >= 4X
There is a 0% 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 4999626 0.02005863006455659 0.5617254093510433
chr2 243199373 8162052 0.03356115560380166 18.84707225033807
chr3 198022430 6319223 0.03191165263450206 0.18654800895780044
chr4 191154276 2364462 0.012369391098528186 0.12544308261673118
chr5 180915260 3363345 0.018590720318451853 0.14405561101296968
chr6 171115067 5116225 0.02989932499631958 0.22806280032793838
chr7 159138663 4703843 0.029558140751754336 0.4503682762498103
chr8 146364022 4593532 0.03138429743342254 0.3239525957530223
chr9 141213431 3167876 0.022433248576758963 0.2107016523322587
chr10 135534747 2109315 0.015562909487705024 0.21655649389170697
chr11 135006516 2161198 0.016008101416379043 0.22807809906204152
chr12 133851895 2379516 0.0177772305726415 0.14248065800984558
chr13 115169878 2297324 0.019947264335905608 0.14694035281602616
chr14 107349540 2471516 0.02302307024324464 0.19941376954097323
chr15 102531392 1103619 0.010763718101086544 0.10882974728268692
chr16 90354753 1656294 0.018331011319349187 0.16220100163807857
chr17 81195210 1246398 0.015350634600243045 0.1379652672128017
chr18 78077248 1451626 0.018592176814428707 0.40676972549935286
chr19 59128983 1234103 0.02087137199704585 0.3339163505915586
chr20 63025520 1337431 0.02122046751855439 0.15732016430364476
chr21 48129895 1223541 0.02542164282718672 0.17684445511334165
chr22 51304566 498164 0.009709934979276504 0.10173073656200138
chrMT 16571 26278 1.5857823909239033 1.5073660931479511
chrX 155270560 2033053 0.01309361542844954 0.1343157203538866
chrY 59373566 157963 0.0026604937288085407 0.07250816171657347