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 |
860,884 |
T→C |
48.3% |
S339S (TCA→TCG) |
trpE ← |
component I of anthranilate synthase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 860,884 | 0 | T | C | 48.3%
| ‑2.0
/ 49.8
| 58 | S339S (TCA→TCG) | trpE | component I of anthranilate synthase |
| Reads supporting (aligned to +/- strand): ref base T (11/19); new base C (12/16); total (23/35) |
| Fisher's exact test for biased strand distribution p-value = 7.89e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.47e-01 |
GTTCAGACAGCTCTTTATGATCGGTACGCATTTCCAGTTCAATACGGCTGTCGAGATCTCTGTCCAGTGAACCATCGGCGCGACGACCGCGTGGGCGTGTTCCGGCAATCGGGTAGATCTCA > minE/860817‑860938
|
gTTCAGACAGCTCTTTATGATCGGTACGCATTTCCAGTTCAATACGTCTGTCGAGATCTCTGTCCAGTg < 1:391299/69‑1 (MQ=255)
gTTCAGACAGCTCTTTATGATCGGTACGCATTTCCAGTTCAATACGGCTGTCGAGATCTCTGTCCAGtc < 1:2684958/69‑2 (MQ=255)
gTTCAGACAGCTCTTTATGATCGGTACGCATTTCCAGTTCAATACGGCTGTCGAGATCTCTGTCCAGTg < 1:1016324/69‑1 (MQ=255)
gTTCAGACAGCTCTTTATGATCGGTACGCATTTCCAGTTCAATACGGCTGTCGAGATCTCTGTCCAGTg < 1:1084000/69‑1 (MQ=255)
gTTCAGACAGCTCTTTATGATCGGTACGCATTTCCAGTTCAATACGGCTGTCGAGATCTCTGTCCAGTg < 1:602150/69‑1 (MQ=255)
gTTCAGACAGCTCTTTATGATCGGTACGCATTTCCAGTTCAATACGGCTGTCGAGATCTCTGTCCAGTg < 1:2771760/69‑1 (MQ=255)
gTTCAGACAGCTCTTTATGATCGGTACGCATTTCCAGTTCAATACGGCTGTCGAGATCTCTGTCCAGTg < 1:2530049/69‑1 (MQ=255)
gTTCAGACAGCTCTTTATGATCGGTACACATTTCCAGTTCAATACGGCTGTCGAGATCTCTGTCCAGTg < 1:3124248/69‑1 (MQ=255)
ttCAGACAGCTCTTTATGATCGGTACGCATTTCCAGTTCAATACGGCTGTCGAGATCTCTGTCCAGTg < 1:2660456/68‑1 (MQ=255)
ttCAGACAGCTCTTTATGATCGGTACGCATTTCCAGTTAAATACGGCTGTCGAGATCTCTGTCCAGTg < 1:1568619/68‑1 (MQ=255)
tCCAGTTCAATACGGCTGTCGAGATCTCTGTCCAGTGAACCATCg > 1:891967/1‑45 (MQ=255)
tCCAGTTCAATACGGCTGTCGAGATCTCTGTCCAGTGAACCATCGGCGCGCCGACCGCGTGGGCGTGtt > 1:1950235/1‑69 (MQ=255)
tCCAGTTCAATACGGCTGTCGAGATCTCTGTCCAGTGAACCATCGGCGCGACGACCGCGTGGGCGTGtt > 1:2477674/1‑69 (MQ=255)
tCCAGTTCAATACGGCTGTCGAGATCTCTGTCCAGTGAACCATCGGCGCGACGACCGCGTGGGCGTGtt > 1:2212732/1‑69 (MQ=255)
cAATACGGCTGTCGAGGTCTCTGTCCAGTGAACCATCGGCGCGACGACCGCGTGGGCGTGTTCCGGCaa < 1:984551/69‑1 (MQ=255)
cAATACGGCTGTCGAGATCTCTGTCCAGTGAACCATCGGCGCGACGACCGCGTGGGCGTGTTCCGGCaa < 1:526465/69‑1 (MQ=255)
cAATACGGCTGTCGAGATCTCTGTCCAGTGAACCATCGGCGCGACGACCGCGTGGGCGTGTTCCGGCaa < 1:2775642/69‑1 (MQ=255)
cAATACGGCTGTCGAGATCTCTGTCCAGTGAACCATCGGCGCGACGACCGCGTGGGCGTGTTCCGGCaa < 1:2948501/69‑1 (MQ=255)
cAATACGGCTGTCGAGATCTCTGTCCAGTGAACCATCGGCGCGACGACCGCGTGGGCGTGTTCCGGCaa < 1:2546400/69‑1 (MQ=255)
cAATACGGCTGTCGAGATCTCTGTCCAGTGAACCATCGGCGCGACGACCGCGTGGGCGTGTTCCGGCaa < 1:896199/69‑1 (MQ=255)
cAATACGGCTGTCGAGATCTCTGTCCAGTGAACCATCGGCGCGACGACCGCGTGGGCGTGTTCCGGCaa < 1:1041054/69‑1 (MQ=255)
aCGGCTGTCGAGATCTCTGTCCAGTGAACCATCGGCGCGACGACCGCGTGGGCGTGTTCCGGCAATCg > 1:2189140/1‑68 (MQ=255)
aCGGCTGTCGAGATCTCTGTCCAGTGAACCATCGGCGCGACGACCGCGTGGGCGTGTTCCGGCAATCg > 1:2196463/1‑68 (MQ=255)
aCGGCTGTCGAGATCTCTGTCCAGTGAACCATCGGCGCGACGACCGCGTGGGCGTGTTCCGGCAATCg > 1:2358693/1‑68 (MQ=255)
gCTGTCGAGGTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAATCGGGTa < 1:643421/69‑1 (MQ=255)
gCTGTCGAGGTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAATCGGGTa < 1:549794/69‑1 (MQ=255)
gCTGTCGAGGTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAATCGGGTa < 1:2882868/69‑1 (MQ=255)
gCTGTCGAGGTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAATCGGGTa < 1:494994/69‑1 (MQ=255)
gCTGTCGAGGTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAATCGGGTa < 1:1414630/69‑1 (MQ=255)
gCTGTCGAGGTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAATCGGGTa < 1:3180724/69‑1 (MQ=255)
gCTGTCGAGGTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAATCGGGTa < 1:811797/69‑1 (MQ=255)
gCTGTCGAGGTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAATCGGGTa < 1:2801693/69‑1 (MQ=255)
gCTGTCGAGGTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAATCGGGTa < 1:1439586/69‑1 (MQ=255)
gCTGTCGAGGTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAATCGGGTa < 1:2165148/69‑1 (MQ=255)
gCTGTCGAGGTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAATCGGGTa < 1:1837426/69‑1 (MQ=255)
gCTGTCGAGGTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAATCGGGTa < 1:1793868/69‑1 (MQ=255)
gCTGTCGAGGTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAATCGGGTa < 1:1812409/69‑1 (MQ=255)
gCTGTCGAGGTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAAGCGGGTa < 1:441548/69‑1 (MQ=255)
gCTGGCGAGGTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAATCGGGTa < 1:2471902/69‑1 (MQ=255)
gaggTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAATCGGGTAAAtctc > 1:1859136/1‑69 (MQ=255)
gaggTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAATCGGGTAAAtctc > 1:2138887/1‑69 (MQ=255)
gaggTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAATCGGGTAAAtctc > 1:1115292/1‑69 (MQ=255)
gaggTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAATCGGGTAAAtctc > 1:2167220/1‑69 (MQ=255)
gaggTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAATCGGGTAAAtctc > 1:115005/1‑69 (MQ=255)
gaggTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAATCGGGTAAAtctc > 1:2178465/1‑69 (MQ=255)
gaggTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAATCGGGTAAAtctc > 1:1435493/1‑69 (MQ=255)
gaggTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAATCGGGTAAAtctc > 1:1750680/1‑69 (MQ=255)
gaggTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAATCGGGTAAAtctc > 1:1863052/1‑69 (MQ=255)
gaggTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAATCGGGTAAAtctc > 1:153102/1‑69 (MQ=255)
gaggTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAATCGGGTAAAtctc > 1:2699539/1‑69 (MQ=255)
gaggTCTCTGTCCAGCGAACCATCGGCACGACGACCGCGTGGACGTGTTCCGGCAATCGGGTAAAtct > 1:3126606/1‑68 (MQ=255)
gagaTCTCTGTCCAGTGAACCATCGGCGCGACGACCGCGTGGGCGTGTTCCGGCAATCgg > 1:283142/1‑60 (MQ=255)
gagaTCTCTGTCCAGTGAACCATCGGCGCGACGACCGCGTGGGCGTGTTCCGGCAATCGGGTAGAtctc > 1:318677/1‑69 (MQ=255)
gagaTCTCTGTCCAGTGAACCATCGGCGCGACGACCGCGTGGGCGTGTTCCGGCAATCGGGTAGAtctc > 1:954054/1‑69 (MQ=255)
gagaTCTCTGTCCAGTGAACCATCGGCGCGACGACCGCGTGGGCGTGTTCCGGCAATCGGGTAGAtctc > 1:965557/1‑69 (MQ=255)
gaTCTCTGTCCAGTGAACCATCGGCGCGACGACCGCGTGGGCGTGTTCCGGCAATCGGGTAGATCTCa < 1:2860483/68‑1 (MQ=255)
gaTCTCTGTCCAGTGAACCATCGGCGCGACGACCGCGTGGGCGTGTTCCGGCAATCGGGTAGATCTCa < 1:816996/68‑1 (MQ=255)
gaTCTCTGTCCAGTGAACCATCGGCGCGACGACCGCGTGGGCGTGTTCCGGCAATCGGGTAGATCTCa < 1:935797/68‑1 (MQ=255)
ccAGCGAACCATCGGCACGAAGACCGCGTGGACGTGTTCCGGCAATCGGGTa < 1:743003/52‑1 (MQ=255)
|
GTTCAGACAGCTCTTTATGATCGGTACGCATTTCCAGTTCAATACGGCTGTCGAGATCTCTGTCCAGTGAACCATCGGCGCGACGACCGCGTGGGCGTGTTCCGGCAATCGGGTAGATCTCA > minE/860817‑860938
|
| 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
