BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6237570.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 = 1,621,451
number of mapped reads = 1,294,769 (79.85%)
number of supplementary alignments = 7,465 (0.46%)
number of secondary alignments = 0
number of mapped bases = 80,259,845 bp
number of sequenced bases = 80,212,817 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 72,673
duplication rate = 3.86%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 42.1436
>>>>>>> ACTG content
number of A's = 20,685,678 bp (25.79%)
number of C's = 14,286,513 bp (17.81%)
number of T's = 25,611,713 bp (31.93%)
number of G's = 19,615,497 bp (24.45%)
number of N's = 13,416 bp (0.02%)
GC percentage = 42.27%
>>>>>>> Mismatches and indels
general error rate = 0.0098
number of mismatches = 770,394
number of insertions = 7,509
mapped reads with insertion percentage = 0.57%
number of deletions = 29,295
mapped reads with deletion percentage = 2.23%
homopolymer indels = 46.69%
>>>>>>> Coverage
mean coverageData = 0.0259X
std coverageData = 0.2778X
There is a 2.19% of reference with a coverageData >= 1X
There is a 0.24% of reference with a coverageData >= 2X
There is a 0.06% of reference with a coverageData >= 3X
There is a 0.03% 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 0.01% 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 6808718 0.027316754408407272 0.44327005472438474
chr2 243199373 6297326 0.02589367695450432 0.3830821490018234
chr3 198022430 5237895 0.02645101870530525 0.20169737439963314
chr4 191154276 4847506 0.025359129293032398 0.20489162093228688
chr5 180915260 4732504 0.026158677825187326 0.19763587421110418
chr6 171115067 4406180 0.025749807291955185 0.2226234662133907
chr7 159138663 4607368 0.028951908437235017 0.3216809705407622
chr8 146364022 4531200 0.030958427748043162 0.333185503851509
chr9 141213431 3476402 0.024618069084377674 0.259751387723729
chr10 135534747 3917069 0.028900847101592332 0.2607335767274628
chr11 135006516 3293598 0.02439584471611726 0.23285680133837183
chr12 133851895 4304618 0.03215955963865883 0.221718168865268
chr13 115169878 2754937 0.02392063834607865 0.19266255845048538
chr14 107349540 2380231 0.02217271727480155 0.20683641320937055
chr15 102531392 2245647 0.02190204342490542 0.18709952468411273
chr16 90354753 2105169 0.023298929277134985 0.2046462925603876
chr17 81195210 2092656 0.025773145977453595 0.20067071217245316
chr18 78077248 2190469 0.028055151226641595 0.43675067970975934
chr19 59128983 1523029 0.025757740497583056 0.3222363177841101
chr20 63025520 1636896 0.02597195548723755 0.2124629657092272
chr21 48129895 1091256 0.02267314316808711 0.19913594313327543
chr22 51304566 857484 0.016713600111148003 0.15416681987309486
chrMT 16571 43424 2.620481564178384 3.2826517461520632
chrX 155270560 4601548 0.029635675945266123 0.24694237580933473
chrY 59373566 276715 0.004660575718157134 0.12034995253506416