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 |
2,066,109 |
A→C |
38.6% |
T26T (ACT→ACG) |
ygjF ← |
G/U mismatch‑specific DNA glycosylase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,066,109 | 0 | A | C | 38.6%
| 38.1
/ 64.0
| 70 | T26T (ACT→ACG) | ygjF | G/U mismatch‑specific DNA glycosylase |
| Reads supporting (aligned to +/- strand): ref base A (26/17); new base C (11/16); total (37/33) |
| Fisher's exact test for biased strand distribution p-value = 1.42e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GGTAAACCCGGCCTGATATATCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAGGGTTGATACCGCAAAACACGACCCGTAACCCTGGAGCCAAAATATC > minE/2066046‑2066177
|
ggtAAACCCGGCCTGATATATCACCTTCCAGAAGCGGTTTGCCGGATGAGCAAAGGGAAAACCCGttc > 1:514589/1‑66 (MQ=255)
ggtAAACCCGGCCTGATATATCACCTTCCAGAAGCGGTTTGCCGGATGAGCAAAGGGAAAACCCGttc > 1:1467009/1‑66 (MQ=255)
ggtAAACCCGGCCTGATATATCACCTTCCAGAAGCGGTTTGCCGGATGAGCAAAGGGAAAACCCGttc > 1:1290931/1‑66 (MQ=255)
ggtAAACCCGGCCTGATATATCACCTTCCAGAAGCGGTTTGCCGGATGAGCAAAGGGAAAACCCGTtcc > 1:1039530/1‑69 (MQ=255)
ggtAAACCCGGCCTGATATATCACCTTCCAGAAGCGGTTTGCCGGATGAGCAAAGGGAAAACCCGTtcc > 1:1852599/1‑69 (MQ=255)
ggtAAACCCGGCCTGATATATCACCTTCCAGAAGCGGTTTGCCGGATGAGCAAAGGGAAAACCCGTtcc > 1:1765100/1‑69 (MQ=255)
ggtAAACCCGGCCTGATATATCACCTTCCAGAAGCGGTTTGCCGGATGAGCAAAGGGAAAACCCGTtcc > 1:2261401/1‑69 (MQ=255)
ggtAAACCCGGCCTGATATATCACCTTCCAGAAGCGGTTTGCCGGATGAGCAAAGGGAAAACCCGTtcc > 1:269199/1‑69 (MQ=255)
ggtAAACCCGGCCTGATATATCACCTTCCAGAAGCGGTTTGCCGGATGAGCAAAGGGAAAACCCGTtcc > 1:2774412/1‑69 (MQ=255)
ggtAAACCCGGCCTGATATATCACCTTCCAGAAGCGGTTTGCCGGATGAGCAAAGGGAAAACCCGTtcc > 1:3328980/1‑69 (MQ=255)
ggtAAACCCGGCCTGATATATCACCTTCCAGAAGCGGTTTGCCGGATGAGCAAAGGGAAAACCCGTtcc > 1:3396939/1‑69 (MQ=255)
gATATATCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGcc < 1:2976319/69‑1 (MQ=255)
gATATATCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGcc < 1:2808552/69‑1 (MQ=255)
gATATATCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGcc < 1:1108081/69‑1 (MQ=255)
gATATATCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGcc < 1:1036239/69‑1 (MQ=255)
atatCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTcc > 1:3103257/1‑51 (MQ=255)
atatCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTc > 1:1505359/1‑50 (MQ=255)
atatCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCa > 1:1736870/1‑68 (MQ=255)
atatCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAg > 1:745054/1‑69 (MQ=255)
atatCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAg > 1:925232/1‑69 (MQ=255)
atatCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAg > 1:2022049/1‑69 (MQ=255)
atatCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAg > 1:2331798/1‑69 (MQ=255)
atatCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAg > 1:1213359/1‑69 (MQ=255)
atatCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAg > 1:1792608/1‑69 (MQ=255)
tCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAggg < 1:1823217/68‑1 (MQ=255)
tCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAggg < 1:1315703/68‑1 (MQ=255)
tCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAggg > 1:3094619/1‑68 (MQ=255)
tCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAggg < 1:1391873/68‑1 (MQ=255)
tCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAggg < 1:3432512/68‑1 (MQ=255)
tCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAggg > 1:2767201/1‑68 (MQ=255)
tCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAggg < 1:247073/68‑1 (MQ=255)
tCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAggg < 1:236472/68‑1 (MQ=255)
tCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAggg < 1:1731063/68‑1 (MQ=255)
tCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAggg < 1:931651/68‑1 (MQ=255)
tCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAggg > 1:2079757/1‑68 (MQ=255)
tCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGG‑AAACCAGTCCCGGCGGATGAAAGCCCAGGGtt > 1:1948795/1‑69 (MQ=255)
cTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAGGGTTGAt < 1:1952610/69‑1 (MQ=255)
cTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAGGGTTGAt < 1:1463644/69‑1 (MQ=255)
cTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAGGGTTGAt < 1:1823859/69‑1 (MQ=255)
ttCCAGAAGCGATTTGCCGGATTAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAGGGTTGAt < 1:2183128/68‑1 (MQ=255)
aGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAGGGtt < 1:2037352/58‑1 (MQ=255)
gCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAGGGTTGATACCGCaaaa > 1:1982791/1‑69 (MQ=255)
ttGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAGGGTTGATACCGCAAAACACg > 1:1068563/1‑68 (MQ=255)
ttGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAGGGTTGATACCGCAAAACACGa > 1:1628172/1‑69 (MQ=255)
ttGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAGGGTTGATACCGCAAAACACGa > 1:1234458/1‑69 (MQ=255)
ttGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAGGGTTGATACCGCAAAACACGa > 1:2181176/1‑69 (MQ=255)
tGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAGGGTTGATACCGCAAAACACGACCCGTAAc > 1:3424549/1‑69 (MQ=255)
tGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAGGGTTGATACCGCAAAACACGACCCGTAAc > 1:3194088/1‑69 (MQ=255)
tGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAGGGTTGATACCGCAAAACACGACCCGTAAc > 1:3367664/1‑69 (MQ=255)
tGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAGGGTTGATACCGCAAAACACGACCCGTAAc > 1:3367666/1‑69 (MQ=255)
tGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAGGGTTGATACCGCAAAACACGACCCGTAAc > 1:3423613/1‑69 (MQ=255)
tGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAGGGTTGATACCGCAAAACACGACCCGTAAc > 1:416213/1‑69 (MQ=255)
tGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAGGGTTGATACCGCAAAACACGACCCGTAAc > 1:1996075/1‑69 (MQ=255)
gAGCAAAGGGAAAACCCGTTCCGGCGGATGAAAGACCAGGGtt < 1:586176/43‑1 (MQ=25)
gAGCAAAGGGAAAACCCGTTCCGGCGGATGAAAGACCAGGGtt < 1:699172/43‑1 (MQ=25)
gAGCAAAGGGAAAACCCGTTCCGGCGGATGAAAGACCAGGGtt < 1:732256/43‑1 (MQ=25)
gAGCAAAGGGAAAACCCGTTCCGGCGGATGAAAGACCAGGGtt < 1:1090890/43‑1 (MQ=25)
gAGCAAAGGGAAAACCCGTTCCGGCGGATGAAAGACCAGGGtt < 1:823629/43‑1 (MQ=25)
gAGCAAAGGGAAAACCCGTTCCGGCGGATGAAAGACCAGGGtt < 1:939177/43‑1 (MQ=25)
gAGCAAAGGGAAAACCCGTTCCGGCGGATGAAAGACCAGGGtt < 1:1234515/43‑1 (MQ=25)
gAGCAAAGGGAAAACCCGTTCCGGCGGATGAAAGACCAGGGtt < 1:3293327/43‑1 (MQ=25)
gAGCAAAGGGAAAACCCGTTCCGGCGGATGAAAGACCAGGGtt < 1:3151517/43‑1 (MQ=25)
gAGCAAAGGGAAAACCCGTTCCGGCGGATGAAAGACCAGGGtt < 1:3025174/43‑1 (MQ=25)
gAGCAAAGGGAAAACCCGTTCCGGCGGATGAAAGACCAGGGtt < 1:1542755/43‑1 (MQ=25)
gAGCAAAGGGAAAACCCGTTCCGGCGGATGAAAGACCAGGGtt < 1:2663245/43‑1 (MQ=25)
gAGCAAAGGGAAAACCCGTTCCGGCGGATGAAAGACCAGGGtt < 1:2556887/43‑1 (MQ=25)
gAGCAAAGGGAAAACCCGTTCCGGCGGATGAAAGACCAGGGtt < 1:2516784/43‑1 (MQ=25)
gAGCAAAGGGAAAACCCGTTCCGGCGGATGAAAGACCAGGGtt < 1:2133941/43‑1 (MQ=25)
gAGCAAAGGGAAAACCCGTTCCGGCGGATGAAAGACCAGGGtt < 1:2024493/43‑1 (MQ=25)
aGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAGGGTTGATACCGCAAAACACGACCCGTAAccc > 1:1679370/1‑69 (MQ=255)
aGTCCCGGCGGATGAAAGCCCAGGGTTGATACCGCAAAACACGACCCGTAACCCTGGAGCCAAAATATc < 1:3422145/69‑1 (MQ=255)
aGTCCCGGCGGATGAAAGCCCAGGGTTGATACCGCAAAACACGACCCGTAACCCTGGAGCCAAAATATc < 1:39343/69‑1 (MQ=255)
aGTCCCGGCGGATGAAAGCCCAGGGTTGATACCGCAAAACACGACCCGTAACCCTGGAGCCAAAATATc < 1:310655/69‑1 (MQ=255)
|
GGTAAACCCGGCCTGATATATCACCTTCCAGAAGCGATTTGCCGGATGAGCAAAGGGAAAACCAGTCCCGGCGGATGAAAGCCCAGGGTTGATACCGCAAAACACGACCCGTAACCCTGGAGCCAAAATATC > minE/2066046‑2066177
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
