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 |
2,441,954 |
T→C |
22.6% |
S443S (TCA→TCG) |
ilvA ← |
threonine deaminase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,441,954 | 0 | T | C | 22.6%
| 84.7
/ 18.8
| 66 | S443S (TCA→TCG) | ilvA | threonine deaminase |
| Reads supporting (aligned to +/- strand): ref base T (31/20); new base C (6/9); total (37/29) |
| Fisher's exact test for biased strand distribution p-value = 2.36e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ATAGTGGAACAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGATGGACGTCCGCCGACCA > minE/2441888‑2442018
|
aTAGTGGAACAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCGGt < 1:1576069/67‑1 (MQ=255)
aTAGTGGAACAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCGGTGa > 1:2574146/1‑69 (MQ=255)
aTAGTGGAACAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCGGTGa > 1:2235431/1‑69 (MQ=255)
aTAGTGGAACAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCGGTGa > 1:853489/1‑69 (MQ=255)
acaaacaaATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCGGTGATTCCGGGa < 1:34130/69‑1 (MQ=255)
aCAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCGGTGATTCCGGGa < 1:1066146/69‑1 (MQ=255)
aCAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCGGTGATTCCGGGa < 1:2964410/69‑1 (MQ=255)
aCAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCGGTGATTCCGGGa > 1:300882/1‑69 (MQ=255)
aCAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCGGTGATTCCGGGa < 1:1953807/69‑1 (MQ=255)
aCAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCGGTGATTCCGGGa > 1:231364/1‑69 (MQ=255)
aCAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCGGTGATTCCGGGa < 1:393259/69‑1 (MQ=255)
aaaTGTTCCAGTGCGTACCCAGCGTGTTGAGGAAGCGCAACAGCGCGCCCGGCGATTCCGGGAATTCGa > 1:2946768/1‑69 (MQ=255)
aaaTGTTCCAGTGCGTACCCAGCGTGTTGAGGAAGCGCAACAGCGCGCCCGGCGATTCCGGGAATTCGa > 1:1058573/1‑69 (MQ=255)
aaaTGTTCCAGTGCGTACCCAGCGTGTTGAGGAAGCGCAACAGCGCGCCCGGCGATTCCGGGAATTCGa > 1:1468367/1‑69 (MQ=255)
aaaTGTTCCAGTGCGTACCCAGCGTGTTGAGGAAGCGCAACAGCGCGCCCGGCGATTCCGGGAATTCGa > 1:554239/1‑69 (MQ=255)
aaaTGTTCCAGTGCGTACCCAGCGTGTTGAGGAAGCGCAACAGCGCGCCCGGCGATTCCGGGAATTCGa > 1:707766/1‑69 (MQ=255)
aaaTGTTCCAGTGCGTACCCAGCGTGTTGAGGAAGCGCAACAGCGCGCCCGGCGATTCCGGGAATTCGa > 1:2664065/1‑69 (MQ=255)
aTGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAg > 1:553474/1‑69 (MQ=255)
cgtacCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCg > 1:2419131/1‑69 (MQ=255)
tgtTGAGGAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACg > 1:1649226/1‑69 (MQ=255)
tgtTGAGGAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACg > 1:1685284/1‑69 (MQ=255)
tgtTGAGGAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACg > 1:3370671/1‑69 (MQ=255)
tgtTGAGGAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACg > 1:1738949/1‑69 (MQ=255)
tgtTGAGGAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACg > 1:638442/1‑69 (MQ=255)
tgtTGAGGAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACg > 1:2053889/1‑69 (MQ=255)
tgtTGAGGAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACg > 1:296913/1‑69 (MQ=255)
gAGGAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAgg > 1:3313140/1‑52 (MQ=255)
gAGGAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGAt > 1:1500447/1‑68 (MQ=255)
ggAAGCGCAGCAGCGCGCCCGGTTATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGc < 1:825986/68‑1 (MQ=255)
ggAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGc < 1:473046/68‑1 (MQ=255)
ggAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGc < 1:521285/68‑1 (MQ=255)
ggAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGc < 1:710204/68‑1 (MQ=255)
ggAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGc < 1:920921/68‑1 (MQ=255)
ggAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGc < 1:2515123/68‑1 (MQ=255)
ggAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGc < 1:2488733/68‑1 (MQ=255)
ggAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGc < 1:1098220/68‑1 (MQ=255)
ggAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGc < 1:1381162/68‑1 (MQ=255)
ggAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGc < 1:141278/68‑1 (MQ=255)
ggAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGc < 1:1483246/68‑1 (MQ=255)
gAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGc < 1:2566101/67‑1 (MQ=255)
gAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGc < 1:2251844/67‑1 (MQ=255)
gAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGa > 1:2559957/1‑69 (MQ=255)
gAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGa > 1:1150545/1‑69 (MQ=255)
gAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGa > 1:783375/1‑69 (MQ=255)
gAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGa > 1:1251769/1‑69 (MQ=255)
gAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGa > 1:642036/1‑69 (MQ=255)
gAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGa > 1:58501/1‑69 (MQ=255)
gAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGa > 1:1411799/1‑69 (MQ=255)
gAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGa > 1:1427187/1‑69 (MQ=255)
gAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGa > 1:1727270/1‑69 (MQ=255)
gAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGa > 1:1847944/1‑69 (MQ=255)
gAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGa > 1:3097958/1‑69 (MQ=255)
gAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGa > 1:2684301/1‑69 (MQ=255)
gAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGa > 1:3388875/1‑69 (MQ=255)
gAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGa > 1:2952678/1‑69 (MQ=255)
gcagcaGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGATGGAc > 1:2461865/1‑69 (MQ=255)
gcagcGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGATGGACGTc < 1:126429/69‑1 (MQ=255)
agcGCGCCCGTTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGc < 1:299065/57‑1 (MQ=255)
ccGGCGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGACGGACGCCCGCCGACCa < 1:2095256/69‑1 (MQ=255)
ccGGCGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGACGGACGCCCGCCGACCa < 1:1102056/69‑1 (MQ=255)
ccGGCGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGACGGACGCCCGCCGACCa < 1:777944/69‑1 (MQ=255)
ccGGCGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGACGGACGCCCGCCGACCa < 1:737309/69‑1 (MQ=255)
ccGGCGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGACGGACGCCCGCCGACCa < 1:1192029/69‑1 (MQ=255)
ccGGCGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGACGGACGCCCGCCGACCa < 1:2042733/69‑1 (MQ=255)
ccGGCGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGACGGACGCCCGCCGACCa < 1:47856/69‑1 (MQ=255)
ccGGCGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGACGGACGCCCGCCGACCa < 1:1470429/69‑1 (MQ=255)
cGGCGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGACGGACGCCCGCCGACCa < 1:2114409/68‑1 (MQ=255)
|
ATAGTGGAACAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCGGTGATTCCGGGAATTCGAAGCTGTAGAGGCGTTCCTGCAACGGATGCGATGGACGTCCGCCGACCA > minE/2441888‑2442018
|
| 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
