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 |
2,628,280 |
T→C |
73.3% |
G250G (GGT→GGC) |
livJ → |
leucine/isoleucine/valine transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,628,280 | 0 | T | C | 73.3%
| 72.2
/ 23.4
| 67 | G250G (GGT→GGC) | livJ | leucine/isoleucine/valine transporter subunit |
| Reads supporting (aligned to +/- strand): ref base T (7/11); new base C (38/11); total (45/22) |
| Fisher's exact test for biased strand distribution p-value = 6.83e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AATCCTGCGTCAGGCACGCGCGGCAGGGCTGAAAACTCAGTTTATGGGGCCGGAAGGTGTGGCTAACGTTTCGCTGTCTAACATTGCGGGCGAATCAGCGGAAGGGCTGCTGGTGACCAAGCCGA > minE/2628223‑2628347
|
aaTCCTGCGTCAGGCACGCGCGGCAGGGCTGAAAACTCAGTTTATGGGGCCGGAAGGTGTGGCTAACGt < 1:2847762/69‑1 (MQ=255)
cAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCt < 1:2840951/69‑1 (MQ=25)
cAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCt < 1:203066/69‑1 (MQ=25)
cAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCt < 1:3325578/69‑1 (MQ=25)
cAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCt < 1:1836526/69‑1 (MQ=25)
cAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCt < 1:329331/69‑1 (MQ=25)
cAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCt < 1:473343/69‑1 (MQ=25)
cAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCt < 1:3034606/69‑1 (MQ=25)
cAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCt < 1:151484/69‑1 (MQ=25)
cAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCt < 1:1359807/69‑1 (MQ=25)
cAGGCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCt < 1:927996/69‑1 (MQ=25)
gCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCTaag > 1:3142369/1‑68 (MQ=21)
gCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCTAAc > 1:1414155/1‑69 (MQ=21)
gCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCTAAc > 1:2864417/1‑69 (MQ=21)
gCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCTAAc > 1:2769484/1‑69 (MQ=21)
gCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCTAAc > 1:59129/1‑69 (MQ=21)
gCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCTAAc > 1:1765653/1‑69 (MQ=21)
gCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCTAAc > 1:1816423/1‑69 (MQ=21)
gCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCTAAc > 1:1346686/1‑69 (MQ=21)
gCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCTAAc > 1:1221242/1‑69 (MQ=21)
gCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCTAAc > 1:3396672/1‑69 (MQ=21)
gCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCTCGCTGTCTAAc > 1:2092205/1‑69 (MQ=21)
gCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGTCGCGCTGTCTAAc > 1:3104365/1‑69 (MQ=21)
gCACGTGCGGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGTGGCTAACGACTCGCTGTCTAAc > 1:1191590/1‑69 (MQ=21)
cACGCGCGGCAGGGCTGAAAACTCAGTTTATGGGGCCGGAAGgtgt > 1:540329/1‑46 (MQ=255)
cACGCGCGGCAGGGCTGAAAACTCAGTTTATGGGGCCGGAAGGTGTGGCTAACGTTTCGCTGTCTAACa > 1:1904070/1‑69 (MQ=255)
cACGCGCGGCAGGGCTGAAAACTCAGTTTATGGGGCCGGAAGGTGTGGCTAACGTTTCGCTGTCTAACa > 1:2147406/1‑69 (MQ=255)
cACGCGCGGCAGGGCTGAAAACTCAGTTTATGGGGCCGGAAGGTGTGGCTAACGTTTCGCTGTCTAACa > 1:325848/1‑69 (MQ=255)
cACGCGCGGCAGGGCTGAAAACTCAGTTTATGGGGCCGGAAGGTGTGGCTAACGTTTCGCTGTCTAACa > 1:1692091/1‑69 (MQ=255)
cgGCAGGGCTGAAAACCCAGTTTATGGGGCCGGAAGGCGGGGCTAACGTCTCGCTGTCt < 1:87247/59‑1 (MQ=21)
aaaCTCAGTTTATGGGGCCGGAAGGTGTGGCTAACGTTTCGCTGTCTAACATTGCGGGCGAATCAGc > 1:1830383/1‑67 (MQ=255)
aaaCTCAGTTTATGGGGCCGGAAGGTGTGGCTAACGTTTCGCTGTCTAACATTGCGGGCGAATCAGc > 1:492646/1‑67 (MQ=255)
aaCTCAGTTTATGGGGCCGGAAGGTGTGGCTAACGTTTCGCTGTCTAACATTGCGGGCGAATCAGCGGa > 1:1591918/1‑69 (MQ=255)
tttATGGGGCCGGAAGGTGTGGCTAACGTTTCGCTGTCTAACATTGCGGGCGAATCAGCGGAAGGgc < 1:3281494/67‑1 (MQ=255)
tttATGGGGCCGGAAGGTGTGGCTAACGTTTCGCTGTCTAACATTGCGGGCGAATCAGCGGAAGGgc < 1:3166888/67‑1 (MQ=255)
tttATGGGGCCGGAAGGTGTGGCTAACGTTTCGCTGTCTAACATTGCGGGCGAATCAGCGGAAGGgc < 1:1792731/67‑1 (MQ=255)
tttATGGGGCCGGAAGGTGTGGCTAACGTTTCGCTGTCTAACATTGCGGGCGAATCAGCGGAAGGgc < 1:2803986/67‑1 (MQ=255)
tttATGGGGCCGGAAGGTGTGGCTAACGTTTCGCTGTATAACATTGCGGGCGAATCAGCGGAAGGgc < 1:2197056/67‑1 (MQ=255)
aaGGTGTGGCTAACGTTTCGCTGTCTAACATTGCGGGCGAATCAGCGGAAGGGCTGCTGGTGACCAAGc < 1:2982148/69‑1 (MQ=255)
aaGGTGTGGCTAACGTTTCGCTGTCTAACATTGCGGGCGAATCAGCGGAAGGGCTGCTGGTGACCAAGc < 1:966135/69‑1 (MQ=255)
aaGGTGTGGCTAACGTTTCGCTGTCTAACATTGCGGGCGAATCAGCGGAAGGGCTGCTGGTGACCAAGc < 1:1299950/69‑1 (MQ=255)
aaGGTGTGGCTAACGTTTCGCTGTCTAACATTGCGGGCGAATCAGCGGAAGGGCTGCTGGTGACCAAGc < 1:2346607/69‑1 (MQ=255)
aGGTGTGGCTAACGTTTCGCTGTCTAACATTGCGGGCGAATCAGCGGAAGGGCTGCTGGTGACCAAGc < 1:2515148/68‑1 (MQ=255)
aGGCGTGGCTAACGTCTCGCTGTCTAACATTGCGGGTGAATCAGca > 1:2327530/1‑45 (MQ=37)
aGGCGTGGCTAACGTCTCGCTGTCTAACATTGCGGGTGAATCAGCAGAAGGGCTGCTGGTGACCAAGc > 1:2784736/1‑68 (MQ=255)
aGGCGTGGCTAACGTCTCGCTGTCTAACATTGCGGGTGAATCAGCAGAAGGGCTGCTGGTGACCAAGc > 1:922711/1‑68 (MQ=255)
aGGCGTGGCTAACGTCTCGCTGTCTAACATTGCGGGTGAATCAGCAGAAGGGCTGCTGGTGACCAAGc > 1:913585/1‑68 (MQ=255)
aGGCGTGGCTAACGTCTCGCTGTCTAACATTGCGGGTGAATCAGCAGAAGGGCTGCTGGTGACCAAGc > 1:893077/1‑68 (MQ=255)
aGGCGTGGCTAACGTCTCGCTGTCTAACATTGCGGGTGAATCAGCAGAAGGGCTGCTGGTGACCAAGc > 1:1382379/1‑68 (MQ=255)
aGGCGTGGCTAACGTCTCGCTGTCTAACATTGCGGGTGAATCAGCAGAAGGGCTGCTGGTGACCAAGc > 1:827712/1‑68 (MQ=255)
aGGCGTGGCTAACGTCTCGCTGTCTAACATTGCGGGTGAATCAGCAGAAGGGCTGCTGGTGACCAAGc > 1:1402698/1‑68 (MQ=255)
aGGCGTGGCTAACGTCTCGCTGTCTAACATTGCGGGTGAATCAGCAGAAGGGCTGCTGGTGACCAAGc > 1:570191/1‑68 (MQ=255)
aGGCGTGGCTAACGTCTCGCTGTCTAACATTGCGGGTGAATCAGCAGAAGGGCTGCTGGTGACCAAGc > 1:1783928/1‑68 (MQ=255)
aGGCGTGGCTAACGTCTCGCTGTCTAACATTGCGGGTGAATCAGCAGAAGGGCTGCTGGTGACCAAGc > 1:447446/1‑68 (MQ=255)
aGGCGTGGCTAACGTCTCGCTGTCTAACATTGCGGGTGAATCAGCAGAAGGGCTGCTGGTGACCAAGc > 1:1930439/1‑68 (MQ=255)
aGGCGTGGCTAACGTCTCGCTGTCTAACATTGCGGGTGAATCAGCAGAAGGGCTGCTGGTGACCAAGc > 1:2146829/1‑68 (MQ=255)
aGGCGTGGCTAACGTCTCGCTGTCTAACATTGCGGGTGAATCAGCAGAAGGGCTGCTGGTGACCAAGc > 1:2164269/1‑68 (MQ=255)
aGGCGTGGCTAACGTCTCGCTGTCTAACATTGCGGGTGAATCAGCAGAAGGGCTGCTGGTGACCAAGc > 1:2411219/1‑68 (MQ=255)
aGGCGTGGCTAACGTCTCGCTGTCTAACATTGCGGGTGAATCAGCAGAAGGGCTGCTGGTGACCAAGc > 1:2441131/1‑68 (MQ=255)
aGGCGTGGCTAACGTCTCGCTGTCTAACATTGCGGGTGAATCAGCAGAAGGGCTGCTGGTGACCAAGc > 1:3067129/1‑68 (MQ=255)
aGGCGTGGCTAACGTCTCGCTGTCTAACATTGCGGGTGAATCAGCAGAAGGGCTGCTGGTGACCAAGc > 1:2637848/1‑68 (MQ=255)
aGGCGTGGCTAACGTCTCGCTGTCTAACATTGCGGGTGAATCAGCAGAAGGGCTGCTGGTGACCAAGc > 1:3028793/1‑68 (MQ=255)
aGGCGTGGCTAACGTCTCGCTGTCTAACATTGCGGGTGAATCAGCAGAAGGGCTGCTGGTGACCAAGc > 1:2730266/1‑68 (MQ=255)
aGGCGTGGCTAACGTCTCGCTGTCTAACATTGCGGGTGAATCAGCAGAAGGGCTGCTGGTGACCAAGc > 1:280416/1‑68 (MQ=255)
aGGCGTGGCTAACGTCTCGCTGTCTAACATTGCGGGTGAATCAGCAGAAGG‑‑‑GCTGGTGACCAAGCCga > 1:1550935/1‑68 (MQ=255)
aGGCGTGGCTAACGTCTCGCTGTATAACATTGCGGGTGAATCAGCAGAAGGGCTGCTGGTGACCAAGc > 1:1775779/1‑68 (MQ=255)
aGGCGTGGCTAACGTCTCGCTGTATAACATTGCGGGTGAATCAGCAGAAGGGCTGCTGGTGACCAAGc > 1:3234008/1‑68 (MQ=255)
aGGCGTGGCTAACGTCTCGCTCTCTAACATTGCGGGTGAATCAGCAGAAGGGCTGCTGGTGACCAAGc > 1:1177197/1‑68 (MQ=255)
|
AATCCTGCGTCAGGCACGCGCGGCAGGGCTGAAAACTCAGTTTATGGGGCCGGAAGGTGTGGCTAACGTTTCGCTGTCTAACATTGCGGGCGAATCAGCGGAAGGGCTGCTGGTGACCAAGCCGA > minE/2628223‑2628347
|
| 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
