BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716612.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 = 1,086,441
number of mapped reads = 997,800 (91.84%)
number of supplementary alignments = 35,078 (3.23%)
number of secondary alignments = 0
number of mapped bases = 75,192,950 bp
number of sequenced bases = 75,165,227 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 17,447
duplication rate = 1.06%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.9809
>>>>>>> ACTG content
number of A's = 18,367,356 bp (24.44%)
number of C's = 15,638,703 bp (20.81%)
number of T's = 22,363,966 bp (29.75%)
number of G's = 18,785,845 bp (24.99%)
number of N's = 9,357 bp (0.01%)
GC percentage = 45.8%
>>>>>>> Mismatches and indels
general error rate = 0.0076
number of mismatches = 560,390
number of insertions = 6,236
mapped reads with insertion percentage = 0.62%
number of deletions = 15,694
mapped reads with deletion percentage = 1.55%
homopolymer indels = 40.26%
>>>>>>> Coverage
mean coverageData = 0.0243X
std coverageData = 0.2226X
There is a 2.22% of reference with a coverageData >= 1X
There is a 0.15% of reference with a coverageData >= 2X
There is a 0.02% of reference with a coverageData >= 3X
There is a 0.01% 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 8022337 0.03218582552699036 0.2502782874471598
chr2 243199373 6151861 0.02529554630060662 0.37324425759395213
chr3 198022430 5918200 0.02988651336113793 0.18828875156601904
chr4 191154276 3030779 0.01585514623800516 0.13929881973403924
chr5 180915260 4355530 0.02407497300117193 0.16660153742549924
chr6 171115067 5118766 0.029914174653012875 0.20402313703823985
chr7 159138663 3625298 0.02278074938960622 0.27752470104440774
chr8 146364022 4259148 0.02909969227273626 0.27910477590645805
chr9 141213431 3209327 0.02272678297859642 0.20595059761793813
chr10 135534747 3719012 0.027439546554065577 0.20871793305271621
chr11 135006516 3410944 0.02526503239295502 0.2067229991914429
chr12 133851895 2871488 0.021452725790695754 0.15600840032593036
chr13 115169878 2244320 0.01948703983171711 0.14823056841871596
chr14 107349540 1603480 0.01493699926427258 0.1367744637097482
chr15 102531392 1592119 0.015528112599895259 0.13248938786348965
chr16 90354753 2422929 0.02681573375558893 0.1891179971548191
chr17 81195210 2941985 0.03623347978285911 0.21916544573091185
chr18 78077248 2236118 0.02863981578858927 0.36626025117289696
chr19 59128983 1530302 0.025880742782266354 0.2291375551412084
chr20 63025520 1479500 0.023474617900812244 0.17175496220847034
chr21 48129895 1415772 0.029415646969518632 0.18821946008589738
chr22 51304566 1220509 0.023789481037613688 0.1686954302540615
chrMT 16571 35282 2.129141270894937 2.2574108437946463
chrX 155270560 2611343 0.016818017530174426 0.15336183818037194
chrY 59373566 166601 0.002805979347779111 0.08279976718844823