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 F17 I0 R1
|
71 |
95.7 |
2922988 |
91.7% |
2680379 |
65.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,397,027 |
G→T |
100% |
P54Q (CCG→CAG) |
corA ← |
magnesium/nickel/cobalt transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,397,027 | 0 | G | T | 78.7%
| 76.2
/ 32.9
| 47 | P54Q (CCG→CAG) | corA | magnesium/nickel/cobalt transporter |
| Reads supporting (aligned to +/- strand): ref base G (3/7); new base T (37/0); total (40/7) |
| Fisher's exact test for biased strand distribution p-value = 1.91e-06 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CTTCGATGTCTTCCAGTTCCGGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGA > minE/2397007‑2397093
|
cTTCGATGTCTTCCAGTTCCGGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCtc < 1:1906956/70‑1 (MQ=255)
cTTCGATGTCTTCCAGTTCCGGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCtc < 1:1186217/70‑1 (MQ=255)
cTTCGATGTCTTCCAGTTCCGGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCtc < 1:2225155/70‑1 (MQ=255)
cTTCGATGTCTTCCAGTTCCGGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCtc < 1:1474023/70‑1 (MQ=255)
cTTCGATGTCTTCCAGTTCCGGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCtc < 1:1531952/70‑1 (MQ=255)
cTTCGATGTCTTCCAGTTCCGGGCGGGTTGCCAGGCTCAGGCCAAGTTCAGATTGTACGCGCAGTCGCtc < 1:1229287/70‑1 (MQ=255)
cTTCGATGTCTTCCAGCTCCGGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCtc < 1:705665/70‑1 (MQ=255)
tCCTGGCGGGTTGCCAGTCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:1035543/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGt > 1:417401/1‑48 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTGCGGTTCGa > 1:862620/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCg > 1:1994350/1‑69 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCg > 1:2532170/1‑69 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:2915282/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:2733227/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:2533845/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:580461/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:2357060/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:2351681/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:2292145/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:2231548/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:845370/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:2143678/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:2096911/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:859289/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:2027862/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:94754/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:1577497/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:1060912/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:1124484/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:1199397/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:1406974/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:1461351/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:152818/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:1915759/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:1579167/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:1598105/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:1708086/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:171619/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:1720531/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:1739515/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:1764426/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:1837562/1‑70 (MQ=255)
tCCTGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:1878284/1‑70 (MQ=255)
tCCTGGCGGGTTGACAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:579656/1‑70 (MQ=255)
tCCGGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGt > 1:1111666/1‑48 (MQ=255)
tCCGGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:2859003/1‑70 (MQ=255)
tCCGGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGa > 1:1368237/1‑70 (MQ=255)
|
CTTCGATGTCTTCCAGTTCCGGGCGGGTTGCCAGGCTCTGGCCAAGTTCAGATTGTACGCGCAGTCGCTCGTCGTCGTCCGGTTCGA > minE/2397007‑2397093
|
| 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
