BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716143.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 = 2,858,561
number of mapped reads = 2,469,302 (86.38%)
number of supplementary alignments = 12,562 (0.44%)
number of secondary alignments = 0
number of mapped bases = 142,214,857 bp
number of sequenced bases = 142,171,505 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 114,290
duplication rate = 3.45%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.4478
>>>>>>> ACTG content
number of A's = 37,256,890 bp (26.21%)
number of C's = 25,458,963 bp (17.91%)
number of T's = 44,425,497 bp (31.25%)
number of G's = 35,029,024 bp (24.64%)
number of N's = 1,131 bp (0%)
GC percentage = 42.55%
>>>>>>> Mismatches and indels
general error rate = 0.0053
number of mismatches = 727,187
number of insertions = 10,355
mapped reads with insertion percentage = 0.42%
number of deletions = 27,573
mapped reads with deletion percentage = 1.11%
homopolymer indels = 42.79%
>>>>>>> Coverage
mean coverageData = 0.0459X
std coverageData = 0.3884X
There is a 3.97% of reference with a coverageData >= 1X
There is a 0.45% of reference with a coverageData >= 2X
There is a 0.07% of reference with a coverageData >= 3X
There is a 0.02% 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 16240132 0.06515583365387081 0.6329725587195574
chr2 243199373 14705417 0.06046650868627034 0.5948626071076356
chr3 198022430 9090554 0.045906688449384246 0.24279832919079644
chr4 191154276 6075663 0.03178408104247692 0.2337673458325374
chr5 180915260 10269968 0.05676673156261114 0.27141610824474255
chr6 171115067 5414408 0.03164191263180816 0.23992951101138119
chr7 159138663 9585906 0.060236185344852367 0.637128632167634
chr8 146364022 6437086 0.043979974805557064 0.3513438631648095
chr9 141213431 3937487 0.02788323300493988 0.2866179052308204
chr10 135534747 6359682 0.04692288981806267 0.31929057090205415
chr11 135006516 6090534 0.04511288921788042 0.3673218919734909
chr12 133851895 5440404 0.04064495314018528 0.23216596981021584
chr13 115169878 4193438 0.036410892091072636 0.21792044784831233
chr14 107349540 3060567 0.028510294501494837 0.20755367942790356
chr15 102531392 6173124 0.06020716074936347 0.2878269900219398
chr16 90354753 4200472 0.04648866673344788 0.2635450202973337
chr17 81195210 5240548 0.06454257584899405 0.3199360427753924
chr18 78077248 4664394 0.05974075828082465 0.6570711704904544
chr19 59128983 2209127 0.03736115332814028 0.4847995726016503
chr20 63025520 3735461 0.059269023087790466 0.2802445679089875
chr21 48129895 1816201 0.037735403328845826 0.23435211056065508
chr22 51304566 1595963 0.031107621103353647 0.19777051205559448
chrMT 16571 11609 0.7005612214108986 0.9663390517378343
chrX 155270560 5335621 0.03436337835066738 0.25853164821211083
chrY 59373566 331091 0.0055764041526493455 0.12632737699084318