Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A1 F2 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,500,063 |
T→G |
intergenic (+113/+444) |
BW25113_RS25830 → / ← fecE |
hypothetical protein/Fe(3+) dicitrate ABC transporter ATP‑binding protein FecE |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,500,063 | 0 | T | G | 97.9%
| 170.2
/ ‑3.7
| 48 | intergenic (+113/+444) | BW25113_RS25830/fecE | hypothetical protein/Fe(3+) dicitrate ABC transporter ATP‑binding protein FecE |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base G (22/25); total (22/26) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01 |
TACCTAAGTAGTAGCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTTTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTCCGTGAATGTCCGCTC > NZ_CP009273/4499982‑4500148
|
tacctaAGTAGTAGCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTa < 1:459398/90‑1 (MQ=255)
ctaAGTAGTAGCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGt < 2:232341/90‑1 (MQ=255)
aaGTAGTAGCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTg > 1:907505/1‑90 (MQ=255)
gtagCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTc > 2:249940/1‑90 (MQ=255)
gtagCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTc > 2:396683/1‑90 (MQ=255)
gtagCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTc < 2:87064/90‑1 (MQ=255)
gtagCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTc > 1:685921/1‑90 (MQ=255)
tagCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCt > 2:43037/1‑90 (MQ=255)
tagCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCt > 1:348441/1‑90 (MQ=255)
agCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTg < 2:262972/90‑1 (MQ=255)
agCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTg > 2:300489/1‑90 (MQ=255)
agCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTg < 1:629573/90‑1 (MQ=255)
aaaCGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATc > 1:196170/1‑90 (MQ=255)
aaCGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCa < 1:434342/90‑1 (MQ=255)
aCGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCAt > 1:110311/1‑90 (MQ=255)
aCGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCAt > 1:379675/1‑90 (MQ=255)
aCGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCAt < 2:824597/90‑1 (MQ=255)
cGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTg > 2:187961/1‑77 (MQ=255)
cGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTg < 1:187961/77‑1 (MQ=255)
gCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTg > 2:323723/1‑90 (MQ=255)
cacaCTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGa > 2:650868/1‑90 (MQ=255)
cacaCTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGa > 1:908322/1‑90 (MQ=255)
cacTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGAtt < 1:480271/90‑1 (MQ=255)
ttttAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATc < 2:637925/90‑1 (MQ=255)
ttttAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATc > 2:620197/1‑90 (MQ=255)
ttttAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATc < 2:203543/90‑1 (MQ=255)
gAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCaa < 2:704161/90‑1 (MQ=255)
cGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCa < 1:650868/90‑1 (MQ=255)
cGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCa < 1:546048/90‑1 (MQ=255)
tGGTCAGAACCTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAAcc < 2:260228/90‑1 (MQ=255)
ggTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCt < 2:379675/90‑1 (MQ=255)
aGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCAtt < 2:908322/90‑1 (MQ=255)
ttCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAAcc < 1:185332/68‑1 (MQ=255)
ttCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAAcc > 2:185332/1‑68 (MQ=255)
ttCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTcc > 2:55862/1‑90 (MQ=255)
gTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTCCGTGa > 2:19083/1‑90 (MQ=255)
gTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTCCGTGa < 1:855281/90‑1 (MQ=255)
gTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTCCGTGa > 1:301392/1‑90 (MQ=255)
gTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTCCGTGa > 2:724168/1‑90 (MQ=255)
gTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTCCGTGa < 1:269831/90‑1 (MQ=255)
ttCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTCCGTGaa > 2:749609/1‑90 (MQ=255)
tCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTCCGTGAAt > 2:672406/1‑90 (MQ=255)
tGGTTGCTTTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTCCGTGAATGTcc < 1:201959/90‑1 (MQ=255)
tGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTCCGTGAATGTcc < 2:468699/90‑1 (MQ=255)
tGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTCCGTGAATGTcc < 1:55862/90‑1 (MQ=255)
tGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTCCGTGAATGTcc < 1:300489/90‑1 (MQ=255)
gTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTCCGTGAATGTCCGc < 2:337204/90‑1 (MQ=255)
tGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTCCGTGAATGTCCGctc < 1:749609/90‑1 (MQ=255)
|
TACCTAAGTAGTAGCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTTTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTCCGTGAATGTCCGCTC > NZ_CP009273/4499982‑4500148
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GCTGCACCTACCTAAGTAGTAGCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTTTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTCCGTGAATGTCCGCTCTGGCACAGAGCGAA > NZ_CP009273/4499974‑4500162
|
GCTGCACCTACCTAAGTAGTAGCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACG < SRR3722072.457661/100‑1 (MQ=60)
CTGCACCTACCTAAGTAGTAGCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGT < SRR3722072.696214/100‑1 (MQ=60)
GCACCTACCTAAGTAGTAGCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTG > SRR3722072.923121/1‑100 (MQ=60)
TACCTAAGTAGTAGCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTC > SRR3722072.698200/1‑100 (MQ=60)
TACCTAAGTAGTAGCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTC < SRR3722072.467821/100‑1 (MQ=60)
ACCTAAGTAGTAGCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCT > SRR3722072.354580/1‑100 (MQ=60)
CAGTAGTAGCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATC < SRR3722072.191227/100‑1 (MQ=60)
AAGTAGTAGCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATC > SRR3722072.199558/1‑100 (MQ=60)
GTAGTAGCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCAT > SRR3722072.112353/1‑100 (MQ=60)
GTAGTAGCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCAT > SRR3722072.386457/1‑100 (MQ=60)
GTAGCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGA > SRR3722072.923954/1‑100 (MQ=60)
AGCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATT < SRR3722072.640814/100‑1 (MQ=60)
AACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATC < SRR3722072.442250/100‑1 (MQ=60)
CACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAA < SRR3722072.488984/100‑1 (MQ=60)
CGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGG < SRR3722072.555872/100‑1 (MQ=60)
CGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGG < SRR3722072.662490/100‑1 (MQ=60)
tataagagacagGGATTAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAA < SRR3722072.188555/88‑1 (MQ=60)
TAGCAATTCCGTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTCCGTGA > SRR3722072.306616/1‑100 (MQ=60)
GTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTCCGTGAATGTCCGCTC < SRR3722072.274422/100‑1 (MQ=60)
GTTCCATGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTCCGTGAATGTCCGCTC < SRR3722072.870045/100‑1 (MQ=60)
TGGTTGCTTTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTCCGTGAATGTCCGCTCTGGCAC < SRR3722072.205442/100‑1 (MQ=60)
TGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTCCGTGAATGTCCGCTCTGGCAC < SRR3722072.305698/100‑1 (MQ=60)
TGGTTGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTCCGTGAATGTCCGCTCTGGCAC < SRR3722072.56879/100‑1 (MQ=60)
TGCTGTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTCCGTGAATGTCCGCTCTGGCACAGAG < SRR3722072.762862/100‑1 (MQ=60)
GTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTCCGTGAATGTCCGCTCTGGCACctgtctct > SRR3722072.118011/1‑92 (MQ=60)
GTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTCCGTGAATGTCCGCTCTGGCACAGAGCGAA > SRR3722072.430108/1‑100 (MQ=60)
|
GCTGCACCTACCTAAGTAGTAGCAAACGCACACTTTTTAGAAAAATCGATGGTCAGAAACTGGATTAGCAATTCCGTTCCATGGTTGCTTTTGATTTACGTTGGCGTCTGATCATTGATTTATCCTCAAAAGCCCAACCTCATTGGTAATGAACCAGCTCCGTGAATGTCCGCTCTGGCACAGAGCGAA > NZ_CP009273/4499974‑4500162
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
