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 |
2,225,948 |
G→C |
40.7% |
V129V (GTG→GTC) |
dusB → |
tRNA‑dihydrouridine synthase B |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,225,948 | 0 | G | C | 40.7%
| 25.6
/ 51.9
| 54 | V129V (GTG→GTC) | dusB | tRNA‑dihydrouridine synthase B |
| Reads supporting (aligned to +/- strand): ref base G (5/27); new base C (16/6); total (21/33) |
| Fisher's exact test for biased strand distribution p-value = 4.06e-05 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.84e-01 |
CGCAAGCTCGCAGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGT > minE/2225880‑2226008
|
cGCAAGCTCGCAGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTg > 1:3263410/1‑69 (MQ=255)
cGCAAGCTCGCAGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTg > 1:1741905/1‑69 (MQ=255)
aaGCTCGCAGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGaa < 1:3112838/68‑1 (MQ=255)
aaGCTCGCAGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGaa < 1:1451857/68‑1 (MQ=255)
aGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGa < 1:2442637/69‑1 (MQ=255)
aGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGa < 1:3264207/69‑1 (MQ=255)
aGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGa < 1:2682993/69‑1 (MQ=255)
aGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGa < 1:2221700/69‑1 (MQ=255)
aGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGa < 1:1267220/69‑1 (MQ=255)
aGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGa < 1:2866045/69‑1 (MQ=255)
aGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTCAATGCAGTGGa > 1:2929809/1‑69 (MQ=255)
aGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTCAATGCAGTGGa > 1:2173854/1‑69 (MQ=255)
aGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTCAATGCAGTGGa > 1:2687030/1‑69 (MQ=255)
aGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTCAATGCAGTGGa > 1:2714496/1‑69 (MQ=255)
aGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTCAATGCAGTGGa > 1:1803651/1‑69 (MQ=255)
aGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTCAATGCAGTGGa > 1:2890455/1‑69 (MQ=255)
aGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTCAATGCAGTGGa > 1:1436559/1‑69 (MQ=255)
aGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTCAATGCAGTGGa > 1:1431528/1‑69 (MQ=255)
aGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTCAATGCAGTGGa > 1:1412942/1‑69 (MQ=255)
aGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTCAATGCAGTGGa > 1:1171980/1‑69 (MQ=255)
aGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTCAATGCAGTGGa > 1:1149648/1‑69 (MQ=255)
tCAGCCCTATTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTg < 1:2757128/63‑1 (MQ=255)
tCAGCCCTATTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTg < 1:109998/63‑1 (MQ=255)
tctTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTa < 1:2423956/69‑1 (MQ=255)
tctTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTa < 1:268537/69‑1 (MQ=255)
tctTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTa < 1:264637/69‑1 (MQ=255)
tctTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTa < 1:957944/69‑1 (MQ=255)
tctTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTa < 1:1055760/69‑1 (MQ=255)
aGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTg < 1:948599/68‑1 (MQ=255)
gTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTAc < 1:1793062/50‑1 (MQ=255)
gTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTAc < 1:829631/50‑1 (MQ=255)
gTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTAc < 1:1069410/50‑1 (MQ=255)
gTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTAc < 1:1116683/50‑1 (MQ=255)
gTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTAc < 1:1835091/50‑1 (MQ=255)
gTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTAc < 1:2343857/50‑1 (MQ=255)
gTTAAATCGATCCTAACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTAc < 1:778250/50‑1 (MQ=255)
aaaTCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTg > 1:1033450/1‑68 (MQ=255)
aaaTCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTg > 1:790609/1‑68 (MQ=255)
aaaTCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTg > 1:2421161/1‑68 (MQ=255)
aaaTCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTg > 1:2661704/1‑68 (MQ=255)
aaaTCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATT‑‑CACCGGCTGGGc > 1:1626182/1‑69 (MQ=255)
aTCCTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAAATTCGCACTGGCTGGGCAcc > 1:3004765/1‑68 (MQ=255)
aTCCTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAAATTCGCACTGGCTGGGCAcc > 1:2329604/1‑68 (MQ=255)
aTCCTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAAATTCGCACTGGCTGGGCAcc > 1:2609043/1‑68 (MQ=255)
aTCCTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAAATTCGCACTGGCTGGGCAcc > 1:2143936/1‑68 (MQ=255)
aTCCTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAAATTCGCACTGGCTGGGCAcc > 1:2525067/1‑68 (MQ=255)
cTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGaa < 1:2822652/69‑1 (MQ=255)
cTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGaa < 1:2014047/69‑1 (MQ=255)
cTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGaa < 1:2328945/69‑1 (MQ=255)
cTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGaa < 1:3189003/69‑1 (MQ=255)
cTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGaa < 1:2710257/69‑1 (MQ=255)
cTTACCGAGGTCGTCAATGCAGTGGACGTTCCTGTTACCCTGAAAATTCGCACTGGCTGGGCACCGGaa < 1:947190/69‑1 (MQ=255)
ttACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTg < 1:3129634/41‑1 (MQ=255)
gAGGTCGTGAATTCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGt < 1:1769532/69‑1 (MQ=255)
gAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGt < 1:1263782/69‑1 (MQ=255)
gAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGt < 1:2158738/69‑1 (MQ=255)
|
CGCAAGCTCGCAGGTTCAGCCCTCTTGCAGTACCCGGATGTCGTTAAATCGATCCTTACCGAGGTCGTGAATGCAGTGGACGTTCCTGTTACCCTGAAGATTCGCACCGGCTGGGCACCGGAACACCGT > minE/2225880‑2226008
|
| 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
