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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,970,345 |
G→A |
34.6% |
D149D (GAC→GAT) |
speB ← |
agmatinase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,970,345 | 0 | G | A | 34.6%
| 54.5
/ 40.5
| 75 | D149D (GAC→GAT) | speB | agmatinase |
| Reads supporting (aligned to +/- strand): ref base G (34/15); new base A (7/19); total (41/34) |
| Fisher's exact test for biased strand distribution p-value = 6.07e-04 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.45e-01 |
CGGTATAGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAGCACGCAGCAGCGGCAGCGTAACAA > minE/1970284‑1970412
|
cgGTATAGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAg < 1:629802/68‑1 (MQ=255)
ggTATAGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAgtg < 1:2318086/69‑1 (MQ=255)
ggTATAGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAgtg < 1:566731/69‑1 (MQ=255)
tataGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAgtg < 1:1617560/67‑1 (MQ=255)
taGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAgtgt > 1:1459129/1‑66 (MQ=255)
taGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTAcc > 1:1085132/1‑69 (MQ=255)
gAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAg > 1:961685/1‑69 (MQ=255)
gAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAg > 1:245730/1‑69 (MQ=255)
gAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAg > 1:124877/1‑69 (MQ=255)
aGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCAt < 1:1142694/69‑1 (MQ=255)
aGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCAt < 1:2451185/69‑1 (MQ=255)
aGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCAt < 1:552676/69‑1 (MQ=255)
gCCGTGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCAtttt > 1:1112333/1‑69 (MQ=255)
gCCGTGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCAtttt > 1:817956/1‑69 (MQ=255)
gCCGTGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCAtttt > 1:2514388/1‑69 (MQ=255)
gCCGTGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCAtttt > 1:1289773/1‑69 (MQ=255)
gCCGTGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCAtttt > 1:305247/1‑69 (MQ=255)
gCCGTGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCAtttt > 1:2928915/1‑69 (MQ=255)
gCCGTGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCAtttt > 1:1753014/1‑69 (MQ=255)
ccGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTg > 1:407117/1‑69 (MQ=255)
tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg < 1:3153102/69‑1 (MQ=255)
tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg < 1:236146/69‑1 (MQ=255)
tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg < 1:843088/69‑1 (MQ=255)
tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg < 1:830361/69‑1 (MQ=255)
tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg < 1:2709940/69‑1 (MQ=255)
tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg < 1:941592/69‑1 (MQ=255)
tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg < 1:32810/69‑1 (MQ=255)
tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg < 1:40637/69‑1 (MQ=255)
tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg < 1:1052721/69‑1 (MQ=255)
tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg < 1:936784/69‑1 (MQ=255)
tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg < 1:7738/69‑1 (MQ=255)
tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg < 1:2256012/69‑1 (MQ=255)
tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg < 1:1583200/69‑1 (MQ=255)
tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg < 1:1058394/69‑1 (MQ=255)
tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg < 1:11975/69‑1 (MQ=255)
tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg < 1:1849621/69‑1 (MQ=255)
tGGTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATATTGCCg < 1:441462/69‑1 (MQ=255)
tGGGCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg < 1:2211694/69‑1 (MQ=255)
ggTCAAATTCACAACCGTTAGCGTAGGTATCGGTGTGGGCATCAAAGTGTACCAACGCCATTTTGCCg < 1:1698364/68‑1 (MQ=255)
ttCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCtt > 1:1837137/1‑69 (MQ=255)
ttCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCtt > 1:2755800/1‑69 (MQ=255)
cacaACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTc > 1:1231747/1‑68 (MQ=255)
cacaACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCg > 1:1956779/1‑69 (MQ=255)
cacaACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCg > 1:1004493/1‑69 (MQ=255)
cacaACAGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCg > 1:438920/1‑69 (MQ=255)
caACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGc < 1:1413585/68‑1 (MQ=255)
caACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGc < 1:1270855/68‑1 (MQ=255)
caACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGc < 1:2237393/68‑1 (MQ=255)
caACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGc < 1:2892205/68‑1 (MQ=255)
cGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAg < 1:884316/69‑1 (MQ=255)
ggTGTGTGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAGCACGCAgcagcggcag > 1:436223/1‑69 (MQ=255)
ggTGTGGGCGTCAAAGTGTACCAGCTCCATTTTGCCGAAATGCTTCGCATGAGCACGCAgcagctgcag > 1:1519271/1‑69 (MQ=255)
ggTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAGCACGCAgcagcggcag > 1:2458651/1‑69 (MQ=255)
ggTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAGCACGCAgcagcggcag > 1:2346351/1‑69 (MQ=255)
ggTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAGCACGCAgcagcggcag > 1:85395/1‑69 (MQ=255)
ggTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAGCACGCAgcagcggcag > 1:2425417/1‑69 (MQ=255)
ggTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAGCACGCAgcagcggcag > 1:2451133/1‑69 (MQ=255)
ggTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAGCACGCAgcagcggcag > 1:1870991/1‑69 (MQ=255)
ggTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAGCACGCAgcagcggcag > 1:557729/1‑69 (MQ=255)
ggTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAGCACGCAgcagcggcag > 1:247791/1‑69 (MQ=255)
ggTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAGCACGCAgcagcggcag > 1:2878211/1‑69 (MQ=255)
ggTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAGCACGCAgcagcggcag > 1:3387983/1‑69 (MQ=255)
ggTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAGCACGCAgcagcggcag > 1:1596995/1‑69 (MQ=255)
ggTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAGCACGCAgcagcggcag > 1:3248715/1‑69 (MQ=255)
ggTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAGCACGCAgcagcggcag > 1:1668823/1‑69 (MQ=255)
gtgGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAGCACGCAgcagcggcagcg > 1:1057252/1‑68 (MQ=255)
gtgGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAGCACGCAGCAGCGGCAGCGt > 1:343168/1‑69 (MQ=255)
gtgGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAGCACGCAGCAGCGGCAGCGt > 1:1339582/1‑69 (MQ=255)
gtgGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAGCACGCAGCAGCGGCAGCGt > 1:2426057/1‑69 (MQ=255)
gtgGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAGCACGCAGCAGCGGCAGCGt > 1:1636957/1‑69 (MQ=255)
gtgGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAGCACGCAGCAGCGGCAGCGt > 1:2343811/1‑69 (MQ=255)
gtgGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAGCACGCAACAGCGGAAGCGt > 1:1187205/1‑69 (MQ=255)
cGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAGCACGCAGCAGCGGCAGCGTAACaa < 1:2925833/69‑1 (MQ=255)
cGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAGCACGCAGCAGCGGCAGCGTAACaa < 1:3003341/69‑1 (MQ=255)
cGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATCAGCACGCAGCAGCGGCAGCGTAACaa < 1:1547936/69‑1 (MQ=255)
|
CGGTATAGAACATAGTGCCGTGGTCAAATTCACAACCGTTCGCATAGGTATCGGTGTGGGCGTCAAAGTGTACCAGCGCCATTTTGCCGAAATGCTTCGCATGAGCACGCAGCAGCGGCAGCGTAACAA > minE/1970284‑1970412
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
