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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,751,237 |
A→G |
V241V (GTT→GTC) |
BW25113_RS13685 ← |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,751,237 | 0 | A | G | 94.7%
| 111.6
/ ‑0.6
| 38 | V241V (GTT→GTC) | BW25113_RS13685 | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (1/1); new base G (16/20); total (17/21) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01 |
CTCAAACTCTGACATTTGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGAACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCCTTCTTTCCTGCACTCC > NZ_CP009273/2751150‑2751325
|
ctcAAACTCTGACATTTGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGAc < 2:625355/90‑1 (MQ=255)
tcAAACTCTGACATTTGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACa > 2:417163/1‑90 (MQ=255)
aaaaCTCTGACATTTGAATAAAATCCCATGGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACag < 1:158562/89‑1 (MQ=255)
aaaCTCTGACATTTGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACaga > 1:156680/1‑90 (MQ=255)
aaCTCTGACATTTGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACagag > 2:523740/1‑90 (MQ=255)
ctGACATTTGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCat < 1:200254/90‑1 (MQ=255)
ctGACATTTGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCat > 2:6845/1‑90 (MQ=255)
ctGACATTTGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGAACAGAGTCat > 1:499187/1‑90 (MQ=255)
ttGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAg < 2:449797/90‑1 (MQ=255)
tGAGTAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGc < 2:119625/90‑1 (MQ=255)
tGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGc > 2:4448/1‑90 (MQ=255)
cccATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACt < 2:551550/90‑1 (MQ=255)
cGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTg < 2:712396/90‑1 (MQ=255)
gTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGaa > 2:538862/1‑90 (MQ=255)
ttCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAAt < 2:97991/90‑1 (MQ=255)
tCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATg > 1:566709/1‑90 (MQ=255)
cGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGa < 1:4448/90‑1 (MQ=255)
tAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGatat < 2:74791/90‑1 (MQ=255)
tAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGatat < 2:429649/90‑1 (MQ=255)
tGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCgc > 1:625892/1‑90 (MQ=255)
tGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCgc > 2:265461/1‑90 (MQ=255)
tGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCgc > 1:317890/1‑90 (MQ=255)
tGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCgc > 1:326266/1‑90 (MQ=255)
cTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCgctt < 1:151260/90‑1 (MQ=255)
cTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTc > 2:336088/1‑45 (MQ=255)
cTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTc < 1:336088/45‑1 (MQ=255)
tATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGt > 1:684438/1‑69 (MQ=255)
tATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGt < 2:684438/69‑1 (MQ=255)
tATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGc > 1:282137/1‑90 (MQ=255)
ttttCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCAc < 2:317890/90‑1 (MQ=255)
ttCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCAccc < 2:566709/90‑1 (MQ=255)
ccACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCctt > 1:56905/1‑90 (MQ=255)
cACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCcttc < 1:36841/90‑1 (MQ=255)
cACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCcttc < 2:282137/90‑1 (MQ=255)
cACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTAGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCcttc < 1:376515/90‑1 (MQ=255)
catcatTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCCTTCTTTc > 1:178564/1‑90 (MQ=255)
tCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCCTTCTTTCCTGCAc < 2:625892/90‑1 (MQ=255)
gAACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCCTTCTTTCCTGCACTcc < 2:499187/90‑1 (MQ=255)
|
CTCAAACTCTGACATTTGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGAACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCCTTCTTTCCTGCACTCC > NZ_CP009273/2751150‑2751325
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GATTATTTATCTCAAACTCTGACATTTGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGAACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCCTTCTTTCCTGCACTCCGCCTG > NZ_CP009273/2751140‑2751330
|
GATTATTTATCTCAAACTCTGACATTTGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGAC < SRR3722112.202096/100‑1 (MQ=60)
GATTATTTATCTCAAACTCTGACATTTGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGAC < SRR3722112.248947/100‑1 (MQ=60)
TATTTATCTCAAACTCTGACATTTGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGA > SRR3722112.158598/1‑100 (MQ=60)
ATCTCAAACTCTGACATTTGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGAACAGAGTCAT > SRR3722112.506421/1‑100 (MQ=60)
AAAACTCTGACATTTGAATAAAATCCCATGGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAAT < SRR3722112.160507/100‑1 (MQ=60)
CTGACATTTGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTC < SRR3722112.202688/100‑1 (MQ=60)
attcgtcggcagcgtcagatgtgtataagagacagCTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTC < SRR3722112.340179/65‑1 (MQ=60)
CCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATG > SRR3722112.575336/1‑100 (MQ=60)
CGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACAC < SRR3722112.4497/100‑1 (MQ=60)
GTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGC > SRR3722112.635554/1‑100 (MQ=60)
GTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGC > SRR3722112.330151/1‑100 (MQ=60)
GTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGC > SRR3722112.321587/1‑100 (MQ=60)
GCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCctgtctcttat > SRR3722112.695147/1‑89 (MQ=60)
GCTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGC > SRR3722112.285413/1‑100 (MQ=60)
CTACAACCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCC < SRR3722112.153126/100‑1 (MQ=60)
CCTTATTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCCTT > SRR3722112.57602/1‑100 (MQ=60)
TTTTTCCACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCCTTCTTTC > SRR3722112.180749/1‑100 (MQ=60)
ataagagacagATTCGGGACAGAGTCATTAACTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCCTTCTTTCCTG < SRR3722112.637172/89‑1 (MQ=60)
CACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCCTTCTTTCCTGCAC < SRR3722112.37296/100‑1 (MQ=60)
CACCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTAGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCCTTCTTTCCTGCAC < SRR3722112.381399/100‑1 (MQ=60)
CCCATCATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCCTTCTTTCCTGCACTC > SRR3722112.697994/1‑100 (MQ=60)
ATTCGGGACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCCTTCTTTCCTGCACTCCGCCTG > SRR3722112.561310/1‑100 (MQ=60)
|
GATTATTTATCTCAAACTCTGACATTTGAATAAAATCCCATAGCGGTTCGATAAGTTCATTAACTGCTACAACCTTATTTTTCCACCCATCATTCGGAACAGAGTCATTAATTAGCTCAACCAACTTCAGTTGAATGATATGGTACACTTCCGCTTTGCTTTTGCCACCCTTCTTTCCTGCACTCCGCCTG > NZ_CP009273/2751140‑2751330
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
