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 |
1,881,919 |
C→T |
45.5% |
R405R (CGG→CGA) |
relA ← |
(p)ppGpp synthetase I/GTP pyrophosphokinase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,881,919 | 0 | C | T | 45.5%
| 14.2
/ 63.6
| 79 | R405R (CGG→CGA) | relA | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| Reads supporting (aligned to +/- strand): ref base C (20/23); new base T (18/18); total (38/41) |
| Fisher's exact test for biased strand distribution p-value = 8.23e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.69e-01 |
GTCCAGCGGCGTTGATCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATCTCT > minE/1881856‑1881979
|
gTCCAGCGGCGTTGATCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACCCGgtc > 1:192451/1‑69 (MQ=255)
gTCCAGCGGCGTTGATCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACCCGgtc > 1:492320/1‑69 (MQ=255)
gTCCAGCGGCGTTGATCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACCCGgtc > 1:1143312/1‑69 (MQ=255)
gTCCAGCGGCGTTGATCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACCCGgtc > 1:389930/1‑69 (MQ=255)
gTCCAGCGGCGTTGATCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACCCGgtc > 1:3423955/1‑69 (MQ=255)
gTCCAGCGGCGTTGATCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACCCGgtc > 1:977664/1‑69 (MQ=255)
gTCCAGCGGCGTTGATCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACCCGgtc > 1:3246877/1‑69 (MQ=255)
gTCCAGCGGCGTTGATCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACCCGgt > 1:2991033/1‑68 (MQ=255)
cAGCGGCGTTGATCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACCCGgtcgt > 1:2715925/1‑68 (MQ=255)
cAGCGGCGTTGATCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACCCGgtcgt > 1:2983126/1‑68 (MQ=255)
cAGCGGCGTTGATCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACCCGgtcgt > 1:9848/1‑68 (MQ=255)
cAGCGGCGTTGATCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACCCGgtcgt > 1:2244316/1‑68 (MQ=255)
aTCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACTCGgtcgt > 1:2877701/1‑57 (MQ=255)
aTCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACTCGGTCGTCAAAGACCt > 1:3233522/1‑66 (MQ=255)
aTCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACTCGGTCGTCAAAGACCt > 1:1994989/1‑66 (MQ=255)
aTCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACTCGGTCGTCAAAGACCTg > 1:2570011/1‑67 (MQ=255)
aTCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACTCGGTCGTCAAAGACCTg > 1:2694776/1‑67 (MQ=255)
aTCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACTCGGTCGTCAAAGACCTg > 1:222949/1‑67 (MQ=255)
aTCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACTCGGTCGTCAAAGACCTg > 1:2734550/1‑67 (MQ=255)
aTCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACTCGGTCGTCAAAGACCTg > 1:274759/1‑67 (MQ=255)
aTCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACTCGGTCGTCAAAGACCTg > 1:3340596/1‑67 (MQ=255)
aTCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACTCGGTCGTCAAAGACCTg > 1:3417924/1‑67 (MQ=255)
aTCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACTCGGTCGTCAAAGACCTg > 1:606118/1‑67 (MQ=255)
aTCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACTCGGTCGTCAAAGACCTg > 1:2202559/1‑67 (MQ=255)
aTCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACTCGGTCGTCAAAGACCTg > 1:2192827/1‑67 (MQ=255)
aTCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACTCGGTCGTCAAAGACCTg > 1:1111236/1‑67 (MQ=255)
aTCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACTCGGTCGTCAAAGACCTg > 1:218868/1‑67 (MQ=255)
aTCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACTCGGTCGTCAAAGACATg > 1:3083662/1‑67 (MQ=255)
aTCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACTCGCTCGTCAAAGACCt > 1:2206471/1‑66 (MQ=255)
aTCCCGCAGCCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACTCGGTCGTCAAAGACCTg > 1:1892270/1‑67 (MQ=255)
aCCTTTCGGCGTAAAGACGTACACCCGGTCGTGAAAGACCTGACTACGTa > 1:2866447/1‑50 (MQ=255)
aCCTTTCGGCGTAAAGACGTACACCCGGTCGTCAAATACCt > 1:1895904/1‑41 (MQ=255)
aCCTTTCGGCGTAAAGACGTACACCCGGTCGTCAAAGCCCTGACTACGTACTTCGTCGAGCATTTCGc > 1:2250040/1‑68 (MQ=255)
aCCTTTCGGCGTAAAGACGTACACCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGc > 1:699217/1‑68 (MQ=255)
aCCTTTCGGCGTAAAGACGTACACCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGc > 1:1887279/1‑68 (MQ=255)
tttCGGCGTAAAGACGTACACCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGa < 1:831561/69‑1 (MQ=255)
ttCGGCGTAAAGACGTACACCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGa < 1:520273/68‑1 (MQ=255)
gCGTAAAGACGTACACCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCa < 1:2120621/68‑1 (MQ=255)
gCGTAAAGACGTACACCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCa < 1:2019903/68‑1 (MQ=255)
gCGTAAAGACGTACACCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCACCGGAATCa < 1:3302190/68‑1 (MQ=255)
aggTACACCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATctct < 1:296545/67‑1 (MQ=255)
aCGTACACTCGGTCGTCATAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATatct < 1:369976/69‑1 (MQ=255)
aCGTACACTCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATatct < 1:332546/69‑1 (MQ=255)
aCGTACACTCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATatct < 1:3300748/69‑1 (MQ=255)
aCGTACACTCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATatct < 1:1573909/69‑1 (MQ=255)
aCGTACACTCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATatct < 1:3134703/69‑1 (MQ=255)
aCGTACACTCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATatct < 1:693169/69‑1 (MQ=255)
aCGTACACTCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATatct < 1:511969/69‑1 (MQ=255)
aCGTACACTCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATatct < 1:555692/69‑1 (MQ=255)
aCGTACACTCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATatct < 1:648391/69‑1 (MQ=255)
aCGTACACTCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATatct < 1:1092765/69‑1 (MQ=255)
aCGTACACTCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATatct < 1:3180601/69‑1 (MQ=255)
aCGTACACTCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATatct < 1:2416532/69‑1 (MQ=255)
aCGTACACTCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATatct < 1:3096268/69‑1 (MQ=255)
aCGTACACTCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATatct < 1:2443209/69‑1 (MQ=255)
aCGTACACTCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATatct < 1:2492108/69‑1 (MQ=255)
aCGTACACTCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATatct < 1:891205/69‑1 (MQ=255)
aCGTACACTCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATatct < 1:2103647/69‑1 (MQ=255)
aCGTACACTCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATatct < 1:191018/69‑1 (MQ=255)
aCGTACACCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATctct < 1:2363502/69‑1 (MQ=255)
aCGTACACCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATctct < 1:1766339/69‑1 (MQ=255)
aCGTACACCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATctct < 1:13777/69‑1 (MQ=255)
aCGTACACCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATctct < 1:1435057/69‑1 (MQ=255)
aCGTACACCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATctct < 1:1530803/69‑1 (MQ=255)
aCGTACACCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATctct < 1:2316603/69‑1 (MQ=255)
aCGTACACCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATctct < 1:3233602/69‑1 (MQ=255)
cacaCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATctct > 1:3435749/1‑64 (MQ=255)
cacCCGGTCTTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATctct < 1:285962/64‑1 (MQ=255)
cacCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATctct < 1:1027822/64‑1 (MQ=255)
cacCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATctct < 1:998577/64‑1 (MQ=255)
cacCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATctct < 1:685612/64‑1 (MQ=255)
cacCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATctct < 1:603553/64‑1 (MQ=255)
cacCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATctct < 1:441521/64‑1 (MQ=255)
cacCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATctct < 1:3027342/64‑1 (MQ=255)
cacCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATctct < 1:286503/64‑1 (MQ=255)
cacCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATctct < 1:2615441/64‑1 (MQ=255)
cacCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATctct > 1:234621/1‑64 (MQ=255)
cacCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATctct > 1:1481399/1‑64 (MQ=255)
cacCCGGTCGTCAAAGACCTGACGACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATctct > 1:1236339/1‑64 (MQ=255)
cacCCCGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATctct < 1:505735/64‑1 (MQ=255)
|
GTCCAGCGGCGTTGATCCCGCAGGCAAATCAACGACATCACCTTTCGGCGTAAAGACGTACACCCGGTCGTCAAAGACCTGACTACGTACTTCGTCGAGCATTTCGCCGGAATCAGCCATCTCT > minE/1881856‑1881979
|
| 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
