BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716707.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 4,933,922
number of mapped reads = 4,695,569 (95.17%)
number of supplementary alignments = 109,415 (2.22%)
number of secondary alignments = 0
number of mapped bases = 365,584,731 bp
number of sequenced bases = 365,449,044 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 419,731
duplication rate = 6.71%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.9406
>>>>>>> ACTG content
number of A's = 90,651,041 bp (24.81%)
number of C's = 77,532,393 bp (21.22%)
number of T's = 106,474,370 bp (29.14%)
number of G's = 90,776,100 bp (24.84%)
number of N's = 15,140 bp (0%)
GC percentage = 46.06%
>>>>>>> Mismatches and indels
general error rate = 0.0064
number of mismatches = 2,262,796
number of insertions = 28,380
mapped reads with insertion percentage = 0.59%
number of deletions = 64,431
mapped reads with deletion percentage = 1.35%
homopolymer indels = 38.93%
>>>>>>> Coverage
mean coverageData = 0.1181X
std coverageData = 0.7468X
There is a 8.05% of reference with a coverageData >= 1X
There is a 2.19% of reference with a coverageData >= 2X
There is a 0.76% of reference with a coverageData >= 3X
There is a 0.31% of reference with a coverageData >= 4X
There is a 0.14% of reference with a coverageData >= 5X
There is a 0.07% of reference with a coverageData >= 6X
There is a 0.04% of reference with a coverageData >= 7X
There is a 0.03% of reference with a coverageData >= 8X
There is a 0.02% 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 0.01% 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 29646514 0.11894258831154526 1.1161553147241037
chr2 243199373 30811199 0.12669111198736518 0.880652717732803
chr3 198022430 23466597 0.11850474211431503 0.47912123137954143
chr4 191154276 22729397 0.11890603483021223 0.785789069613269
chr5 180915260 21701148 0.11995200404874636 0.4846906628123125
chr6 171115067 20464790 0.11959665714299723 0.5240270035132109
chr7 159138663 19804374 0.12444728155093272 0.9396629007372149
chr8 146364022 18457503 0.12610683108995188 0.7851818787538748
chr9 141213431 15125089 0.10710800589499167 0.6627871240446357
chr10 135534747 17868781 0.13183911429000564 1.0648818904795325
chr11 135006516 16780207 0.1242918304772786 0.7674221282183432
chr12 133851895 16692589 0.12470939615759642 0.50760144255863
chr13 115169878 10982159 0.09535617464142838 0.4340362697820612
chr14 107349540 10976640 0.10225139297289956 0.5331930132525369
chr15 102531392 10752270 0.10486807786633776 0.4578001578051616
chr16 90354753 11758329 0.1301351462938535 0.573497265166789
chr17 81195210 10307026 0.12694130602039208 0.6099781321880063
chr18 78077248 9579001 0.1226862017472747 1.139000147193991
chr19 59128983 7869246 0.13308610432213927 0.840290245562845
chr20 63025520 8388342 0.1330943719306084 0.5680384092210155
chr21 48129895 4967748 0.10321543398339016 0.6695708909285185
chr22 51304566 5237627 0.10208890569311121 0.47010039000935533
chrMT 16571 39842 2.4043208014000363 2.405740296897597
chrX 155270560 19974617 0.1286439425477695 0.5765455276986047
chrY 59373566 1203696 0.020273264368187015 0.7254783717519451