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 |
1,603,274 |
G→A |
61.9% |
A110A (GCC→GCT) |
yfeX ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,603,274 | 0 | G | A | 61.9%
| 29.8
/ 39.7
| 63 | A110A (GCC→GCT) | yfeX | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (8/16); new base A (28/11); total (36/27) |
| Fisher's exact test for biased strand distribution p-value = 3.96e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.64e-01 |
CCCAACGGAAGCCGTGGATCTCTTCTTTCACTTCAATGCAGTCACCAAAGGCTTCCATCGCCGCCTGGGCGACAGAGAAGTTTACGTCGTGACGCAGAGAAAGAATGTGGATCAACACATCGA > minE/1603207‑1603329
|
cccAACGGAAGCCGTGGATCTCTTCTTTCACTTCAATGCAGTCACCAAAGGCTTCCATCGCCGCCTgg > 1:807344/1‑68 (MQ=255)
cccAACGGAAGCCGTGGATCTCTTCTTTCACTTCAATGCAGTCACCAAAGGCTTCCATCGCCGCCTgg > 1:111869/1‑68 (MQ=255)
cccAACGGAAGCCGTGGATCTCTTCTTTCACTTCAATGCAGTCACCAAAGGCTTCCATCGCCGCCTgg > 1:1664545/1‑68 (MQ=255)
cccAACGGAAGCCGTGGATCTCTTCTTTCACTTCAATGCAGTCACCAAAGGCTTCCATCGCCGCCTgg > 1:1657281/1‑68 (MQ=255)
cccAACGGAAGCCGTGGATCTCTTCTTTCACTTCAATGCAGTCACCAAAGGCTTCCATCGCCGCCTgg > 1:2200831/1‑68 (MQ=255)
cccAACGGAAGCCGTGGATCTCTTCTTTCACTTCAATGCAGTCACCAAAGGCTTCCATCGCCGCCTgg > 1:2926776/1‑68 (MQ=255)
cacAACGGAAGCCGTGGATCTCTTCTTTCACTTCAATGCAGTCACCAAAGGCTTCCATCGCCGCCTgg > 1:1596927/3‑68 (MQ=255)
cAACGGAAGCCGTGGATCTCTTCTTTCACTTCAATGCAGTCACCAAAGGCTTCCATCGCCGCCTGGGc > 1:2965467/1‑68 (MQ=255)
cAACGGAAGCCGTGGATCTCTTCTTTCACTTCAATGCAGTCACCAAAGGCTTCCATCGCCGCCTGGGc > 1:1769387/1‑68 (MQ=255)
cAACGGAAGCCGTGGATCTCTTCTTTCACTTCAATGCAGTCACCAAAGGCTTCCATCGCCGCCTGGGc > 1:2456954/1‑68 (MQ=255)
gCAGTCACCAAAGGCTTCCATCGCCGCCTGGGCGACAGAGAAGtt < 1:471068/45‑1 (MQ=255)
gCAGTCACCAAAGGCTTCCATCGCCGCCTGGGCGACAGAGAAGtt < 1:2094302/45‑1 (MQ=255)
gCAGTCACCAAAGGCTTCCATCGCCGCCTGGGCGACAGAGAAGtt < 1:95235/45‑1 (MQ=255)
gCAGTCACCAAAGGCTTCCATCGCCGACTGGGCGACAGAGAAGtt < 1:3274265/45‑1 (MQ=255)
aCCAAAGGCTTCCATCGCCGCCTGGGCGACAGAGAAGTTTACGTCGTGACGCAGagaaagaa < 1:2532979/62‑1 (MQ=255)
aCCAAAGGCTTCCATCGCCGCCTGGGCGACAGAGAAGTTTACGTCGTGACGCAGagaaagaa < 1:3390710/62‑1 (MQ=255)
aCCAAAGGCTTCCATCGCCGCCTGGGCGACAGAGAAGTTTACGTCGTGACGCAGagaaagaa < 1:590872/62‑1 (MQ=255)
aCCAAAGGCTTCCATCGCCGCCTGGGCGACAGAGAAGTTTACGTCGTGACGCAGAGAAAGAATGTgg > 1:1775274/1‑67 (MQ=255)
aCCAAAGGCTTCCATCGCCGCCTGGGCGACAGAGAAGTTTACGTCGTGACGCAGAGAAAGAATGTgg > 1:223445/1‑67 (MQ=255)
aCCAAAGGCTTCCATCGCCGCCTGGGCGACAGAGAAGTTTACGTCGTGACGCAGAGAAAGAATGTGGa > 1:3151881/1‑68 (MQ=255)
aCCAAAGGCTTCCATCGCCGCCTGGGCGACAGAGAAGTTTACGTCGTGACGCAGAGAAAGAATGTGGa > 1:63077/1‑68 (MQ=255)
aCCAAAGGCTTCCATCGCCGCCTGGGCGACAGAGAAGTTTACATCGTGACGCAGAGAAAGAATGTGGa > 1:600134/1‑68 (MQ=255)
cAAAGGCTTCCATCGCCGCCTGGGCGACAGAGAAGTTTACGTCGTGACGCAGAGAAAGAATGTGGATc < 1:15764/68‑1 (MQ=255)
aaGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGAGAAAGACTGTGGa < 1:2816/64‑1 (MQ=255)
aaGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGAGAAAGAATGTGGa < 1:2999388/64‑1 (MQ=255)
aaGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGAGAAAGAATGTGGa < 1:3059031/64‑1 (MQ=255)
aaGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGAGAAAGAATGTGGa < 1:1271022/64‑1 (MQ=255)
aaGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGAGAAAGAATGTGGa < 1:3331374/64‑1 (MQ=255)
aaGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGAGAAAGAATGTGGa < 1:155709/64‑1 (MQ=255)
aaGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGAGAAAGAATGTGGa < 1:484490/64‑1 (MQ=255)
aaGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGAGAAAGAATGTGGa < 1:864872/64‑1 (MQ=255)
aaGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGAGAAAGAATGTGGa < 1:932031/64‑1 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaagaa > 1:111971/1‑57 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaagaa > 1:1142863/1‑57 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaagaa > 1:417791/1‑57 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaagaa > 1:618212/1‑57 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaagaa > 1:1114636/1‑57 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaagaa > 1:3291628/1‑57 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaagaa > 1:3287824/1‑57 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaagaa > 1:3269829/1‑57 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaagaa > 1:878064/1‑57 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaagaa > 1:177270/1‑57 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaagaa > 1:304938/1‑57 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaagaa > 1:1035698/1‑57 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaagaa > 1:1444097/1‑57 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaagaa > 1:1447878/1‑57 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaagaa > 1:2278924/1‑57 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaagaa > 1:2158382/1‑57 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaagaa > 1:2212989/1‑57 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaagaa > 1:2722180/1‑57 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaagaa > 1:2224051/1‑57 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaagaa > 1:2313071/1‑57 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaagaa > 1:1007172/1‑57 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaagaa > 1:249508/1‑57 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaagaa > 1:2268555/1‑57 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaagaa > 1:2329453/1‑57 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaagaa > 1:2980380/1‑57 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaaga > 1:562614/1‑56 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGAGAAAGAATGTGGa < 1:2618757/63‑1 (MQ=255)
aGGCTTCCATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGAAGCagag > 1:1714011/1‑51 (MQ=255)
aGGCTTACATCGCCGCCTGAGCGACAGAGAAGTTCACGTCGTGACGCAGagaaagaa > 1:425651/1‑57 (MQ=255)
aTCGCCGCCTGGGCGACAGAGAAGTTTACGTCGTGACGCAGAGAAAGAATGTGGATCAACACATCGa < 1:1236697/67‑1 (MQ=255)
aTCGCCGCCTGGGCGACAGAGAAGTTTACGTCGTGACGCAGAGAAAGAATGTGGATCAACACATCGa < 1:2675735/67‑1 (MQ=255)
aTCGCCGCCTGGGCGACAGAGAAGTTTACGTCGTGACGCAGAGAAAGAATGTGGATCAACACATCGa < 1:3223093/67‑1 (MQ=255)
aTCGCCGCCTGGGCGACAGAGAAGTTTACGTCGTGACGCAGAGAAAGAATGTGGATCAACACATCGa < 1:215028/67‑1 (MQ=255)
aTCGCCGCCTGGGCGACAGAGAAGTTTACGTCGTGACGCAGAGAAAGAATGTGGATCAACACATCGa < 1:2098250/67‑1 (MQ=255)
aTCGCCGCCTGGGCGACAGAGAAGTTTACGTCGTGACGCAGAGAAAGAATGTGGATCAACACATCGa < 1:3068108/67‑1 (MQ=255)
aTCGCCGCCTGGGCGACAGAGAAGTTTACGTCGTGACGCAGAGAAAGAATGTGGATCAACACATCGa < 1:2039998/67‑1 (MQ=255)
aTCGCCGCCTGGGCGACAGAGAAGTTTACGTCGTGACGCAGAGAAAGAATGTGGATCAACACATCGa < 1:1788709/67‑1 (MQ=255)
ccgccTGAGCGACAGAGAAGTTCACGTCGTGACGCAGAGAAAGAATGTGGa < 1:2904597/51‑1 (MQ=255)
|
CCCAACGGAAGCCGTGGATCTCTTCTTTCACTTCAATGCAGTCACCAAAGGCTTCCATCGCCGCCTGGGCGACAGAGAAGTTTACGTCGTGACGCAGAGAAAGAATGTGGATCAACACATCGA > minE/1603207‑1603329
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
