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 |
2,891,510 |
G→A |
72.2% |
T55T (ACG→ACA) |
ytfQ → |
predicted sugar transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,891,510 | 0 | G | A | 72.2%
| 70.1
/ 26.6
| 68 | T55T (ACG→ACA) | ytfQ | predicted sugar transporter subunit |
| Reads supporting (aligned to +/- strand): ref base G (16/3); new base A (5/44); total (21/47) |
| Fisher's exact test for biased strand distribution p-value = 1.00e-08 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCTGGCGTGCCGCAGAAACCAATGTGGCGAAAAGTGAAGCCGAAAAGCGCGGAATCACGTTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGATTAAAGCGGTACGTTCCTTCGTTGC > minE/2891452‑2891575
|
gCTGGCGTGCCGCAGAAACCAATGTGGCGAAAAGTGAAGCCGAAAAGCGCGGAATCACGTTGAAAATTg > 1:3213716/1‑69 (MQ=255)
gCTGGCGTGCCGCAGAAACCAATGTGGCGAAAAGTGAAGCCGAAAAGCGCGGAATCACGTTGAAAATTg > 1:621017/1‑69 (MQ=255)
gTGCCGCAGAAACCAATGTGGCGAAAAGTGAAGCCGAAAAGCGCGGAATCACGTTGAAAATTGCCGATg > 1:1724891/1‑69 (MQ=255)
cAATGTGGCGAAAAGTGAAGCCGAAAAGCGCGGAATCACGTTGAAAATTGCCGATGGTCAGCAAAAGc > 1:456651/1‑68 (MQ=255)
cAATGTGGCGAAAAGTGAAGCCGAAAAGCGCGGAATCACGTTGAAAATTGCCGATGGTCAGCAAAAGc > 1:1884322/1‑68 (MQ=255)
cAATGTGGCGAAAAGTGAAGCCGAAAAGCGCGGAATCACGTTGAAAATTGCCGATGGTCAGCAAAAGc > 1:1248674/1‑68 (MQ=255)
gtgGCGAAAAGTGAAGCCGAAAAGCGCGGAATCACGTTGAAAATTGCCGATGGTCAGCAAAAGCAGGaa > 1:782248/1‑69 (MQ=255)
gtgGCGAAAAGTGAAGCCGAAAAGCGCGGAATCACGTTGAAAATTGCCGATGGTCAGCAAAAGCAGGaa > 1:1504270/1‑69 (MQ=255)
gtgGCGAAAAGTGAAGCCGAAAAGCGCGGAATCACGTTGAAAATTGCCGATGGTCAGCAAAAGCAGGaa > 1:3289214/1‑69 (MQ=255)
gtgGCGAAAAGTGAAGCCGAAAAGCGCGGAATCACGTTGAAAATTGCCGATGGTCAGCAAAAGCAGGaa > 1:2390276/1‑69 (MQ=255)
gtgGCGAAAAGTGAAGCCGAAAAGCGCGGAATCACGTTGAAAATTGCCGATGGTCAGCAAAAGCAGGaa > 1:3435045/1‑69 (MQ=255)
gtgGCGAAAAGTGAAGCCGAAAAGCGCGGAATCACGTTGAAAATTGCCGATGGTCAGCAAAAGCAGGaa > 1:504831/1‑69 (MQ=255)
gCGAAAAGTTAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGc < 1:2195850/61‑1 (MQ=255)
gCGAAAAGTGAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGc < 1:2202611/61‑1 (MQ=255)
gCGAAAAGTGAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGc < 1:2334348/61‑1 (MQ=255)
gCGAAAAGTGAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGc < 1:2467610/61‑1 (MQ=255)
gCGAAAAGTGAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGc < 1:3377014/61‑1 (MQ=255)
gCGAAAAGTGAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGc < 1:2471643/61‑1 (MQ=255)
gCGAAAAGTGAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGc < 1:2473843/61‑1 (MQ=255)
gCGAAAAGTGAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGc < 1:2157920/61‑1 (MQ=255)
gCGAAAAGTGAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGc < 1:2676050/61‑1 (MQ=255)
gCGAAAAGTGAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGc < 1:2699476/61‑1 (MQ=255)
gCGAAAAGTGAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGc < 1:2967136/61‑1 (MQ=255)
gCGAAAAGTGAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGc < 1:2992275/61‑1 (MQ=255)
gCGAAAAGTGAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGc < 1:3279807/61‑1 (MQ=255)
gCGAAAAGTGAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGc < 1:468991/61‑1 (MQ=255)
gCGAAAAGTGAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGc < 1:958827/61‑1 (MQ=255)
gCGAAAAGTGAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGc < 1:1226193/61‑1 (MQ=255)
gCGAAAAGTGAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGc < 1:910995/61‑1 (MQ=255)
gCGAAAAGTGAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGc < 1:1458693/61‑1 (MQ=255)
gCGAAAAGTGAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGc < 1:162653/61‑1 (MQ=255)
gCGAAAAGTGAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGc < 1:1663606/61‑1 (MQ=255)
gCGAAAAGTGAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGc < 1:478412/61‑1 (MQ=255)
gCGAAAAGTGAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGc < 1:1936952/61‑1 (MQ=255)
gCGAAAAGTGAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGc < 1:1965886/61‑1 (MQ=255)
gAAAAGTGAAGCCGAAAAGCGCGGAATCACGTTGAAAATTGcc > 1:187528/1‑43 (MQ=255)
gAAAAGTGAAGCCGAAAAGCGCGGAATCACGTTGAAAATTGcc > 1:2412806/1‑43 (MQ=255)
gAAAAGTGAAGCCGAAAAGCGCGGAATCACGTTGAAAATTGcc > 1:1587260/1‑43 (MQ=255)
gAAAAGTGAAGCCGAAAAGCGCGGAATCACGTTGAAAATTGc > 1:3039579/1‑42 (MQ=255)
gTGAAGCCGAAAAACGCGGTATCACAGTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGAt > 1:3117506/1‑67 (MQ=38)
gTGAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGAt > 1:1514019/1‑67 (MQ=38)
gTGAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGAt > 1:3363825/1‑67 (MQ=38)
gTGAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGAt > 1:1992872/1‑67 (MQ=38)
gTGAAGCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGAt > 1:2332527/1‑67 (MQ=38)
gCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGATTAAAGCg < 1:2467662/69‑1 (MQ=38)
gCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGATTAAAGCg < 1:94419/69‑1 (MQ=38)
gCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGATTAAAGCg < 1:3289287/69‑1 (MQ=38)
gCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGATTAAAGCg < 1:795336/69‑1 (MQ=38)
gCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGATTAAAGCg < 1:3356358/69‑1 (MQ=38)
gCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGATTAAAGCg < 1:3381915/69‑1 (MQ=38)
gCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGATTAAAGCg < 1:3159808/69‑1 (MQ=38)
gCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGATTAAAGCg < 1:1253982/69‑1 (MQ=38)
gCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGATTAAAGCg < 1:1504902/69‑1 (MQ=38)
gCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGATTAAAGCg < 1:2066138/69‑1 (MQ=38)
gCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGATTAAAGCg < 1:2145176/69‑1 (MQ=38)
gCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGATTAAAGCg < 1:1078506/69‑1 (MQ=38)
gCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGATTAAAGCg < 1:251947/69‑1 (MQ=38)
gCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGATTAAAGCg < 1:2801294/69‑1 (MQ=38)
gCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGATTAAAGCg < 1:3118654/69‑1 (MQ=38)
gCCGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGATTAAAGCg < 1:3237195/69‑1 (MQ=38)
ccGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGATTAAAGCg < 1:2461641/68‑1 (MQ=38)
ccGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGATTAAAGCg < 1:2832111/68‑1 (MQ=38)
ccGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGATTAAAGCg < 1:1718567/68‑1 (MQ=38)
ccGAAAAACGCGGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGATTAAAGCg < 1:1153241/68‑1 (MQ=38)
cgGTATCACACTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGATTAAAGCg < 1:1486236/58‑1 (MQ=38)
cACGTTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGATTAAAGCGGTACGTTCCTTCGTTGc < 1:1892108/69‑1 (MQ=255)
cACGTTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGATTAAAGCGGTACGTTCCTTCGTTGc < 1:1339688/69‑1 (MQ=255)
aCGCTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGATTAAAGCGGTACGTTCCTTCGTTGc < 1:1251694/68‑1 (MQ=255)
|
GCTGGCGTGCCGCAGAAACCAATGTGGCGAAAAGTGAAGCCGAAAAGCGCGGAATCACGTTGAAAATTGCCGATGGTCAGCAAAAGCAGGAAAACCAGATTAAAGCGGTACGTTCCTTCGTTGC > minE/2891452‑2891575
|
| 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
