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 |
2,406,099 |
C→T |
26.5% |
V454V (GTG→GTA) |
cyaA ← |
adenylate cyclase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,406,099 | 0 | C | T | 26.5%
| 49.4
/ 14.2
| 45 | V454V (GTG→GTA) | cyaA | adenylate cyclase |
| Reads supporting (aligned to +/- strand): ref base C (27/6); new base T (2/10); total (29/16) |
| Fisher's exact test for biased strand distribution p-value = 1.18e-04 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01 |
ATCGACTCAATATTTGGCGCGCGGTTATACAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTCCGAGAGATCGGGTGAAATCTGCGGGTTTACCAGCGTCACTTT > minE/2406034‑2406167
|
atCGACTCAATATTTGGCGCGCGGTTATACAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGcac > 1:812741/1‑68 (MQ=255)
atCGACTCAATATTTGGCGCGCGGTTATACAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGcac > 1:3064104/1‑68 (MQ=255)
atCGACTCAATATTTGGCGCGCGGTTATACAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGcac > 1:2263132/1‑68 (MQ=255)
tCAATATTTGGCGCGCGGTTATACAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACataaa > 1:2377397/1‑67 (MQ=255)
tCAATATTTGGCGCGCGGTTATACAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACataaa > 1:224598/1‑67 (MQ=255)
tCAATATTTGGCGCGCGGTTATACAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACataaa > 1:2724908/1‑67 (MQ=255)
tCAATATTTGGCGCGCGGTTATACAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACataaa > 1:1966449/1‑67 (MQ=255)
tatTTGGCGCGCGGTTATACAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAg > 1:773836/1‑68 (MQ=255)
tttGGCGCGCGGTTATACAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAg > 1:773714/1‑66 (MQ=255)
ataCAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTcc > 1:2238041/1‑67 (MQ=255)
ataCAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTcc > 1:2871050/1‑67 (MQ=255)
ataCAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTcc > 1:292599/1‑67 (MQ=255)
ataCAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTcc > 1:1715145/1‑67 (MQ=255)
ataCAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTcc > 1:469966/1‑67 (MQ=255)
ataCAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTcc > 1:526832/1‑67 (MQ=255)
ataCAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTcc > 1:751389/1‑67 (MQ=255)
ataCAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTcc > 1:1567605/1‑67 (MQ=255)
ataCAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTc > 1:852170/1‑66 (MQ=255)
ataCAGATACCAACCTGAACGGTTAGCCCGACCCGGCGGCACATAAATAAAGGTCAGATTCGGTTcc > 1:3134264/1‑67 (MQ=255)
aCAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTcc > 1:2962931/1‑65 (MQ=255)
aCAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTcc > 1:358409/1‑65 (MQ=255)
aCAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTcc > 1:93231/1‑65 (MQ=255)
aCAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTcc > 1:2032660/1‑65 (MQ=255)
aCAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTcc > 1:2160605/1‑65 (MQ=255)
cAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTcc > 1:897867/1‑64 (MQ=255)
cAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTcc > 1:1266674/1‑64 (MQ=255)
cAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTcc > 1:2870942/1‑64 (MQ=255)
cAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTcc > 1:1192753/1‑64 (MQ=255)
cAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTCCgagag < 1:546143/69‑1 (MQ=255)
cAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTCCgagag < 1:814725/69‑1 (MQ=255)
aCCAACCTGAACGGTTGGCGCGGCCCGGCGGTACATAAATAAAGGTCAGa < 1:2062527/50‑1 (MQ=38)
aCCAACCTGAACGGTTGGCGCGGCCCGGCGGTACATAAATAAAGGTCAGa < 1:2988110/50‑1 (MQ=38)
aCCAACCTGAACGGTTGGCGCGGCCCGGCGGTACATAAATAAAGGTCAGa < 1:2259905/50‑1 (MQ=38)
aCCAACCTGAACGGTTGGCGCGGCCCGGCGGTACATAAATAAAGGTCAGa < 1:265302/50‑1 (MQ=38)
aCCAACCTGAACGGTTGGCGCGGCCCGGCGGTACATAAATAAAGGTCAGa < 1:3127897/50‑1 (MQ=38)
aCCAACCTGAACGGTTGGCGCGGCCCGGCGGTACATAAATAAAGGTCAGa < 1:2415086/50‑1 (MQ=38)
aCCAACCTGAACGGTTGGCGCGGCCCGGCGGTACATAAATAAAGGTCAGa < 1:1295072/50‑1 (MQ=38)
aCCAACCTGAACGGTTGGCGCGGCCCGGCGGTACATAAATAAAGGTCAGa < 1:1604454/50‑1 (MQ=38)
aCCAACCTGAACGGTTGGCGCGGCCCGGCGGTACATAAATAAAGGTCAGa < 1:734578/50‑1 (MQ=38)
aCCAACCTGAACGGTTGGCGCGGCCCGGCGGTACATAAATAAAGGTCAGa < 1:511378/50‑1 (MQ=38)
ccAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTGCgaga > 1:3119556/1‑62 (MQ=255)
ccAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTCCGAGAGATCgg > 1:2227908/1‑68 (MQ=255)
aGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTCCGAGAGATCGGGTGAAATCTGCGGGtt < 1:2016471/69‑1 (MQ=255)
aGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTCCGAGAGATCGGGTGAAATCTGCGGGtt < 1:3004530/69‑1 (MQ=255)
cccggcGGTACATAAATAAAGGTCAGATTCGGTTCCGAGAGATCGGGCGAAATCTGCGGGTTTACCAGc > 1:766927/1‑69 (MQ=255)
cccggcGGTACATAAATAAAGGTCAGATTCGGTTCCGAGAGATCGGGCGAAATCTGCGGGTTTACCAGc > 1:908723/1‑69 (MQ=255)
ccggcGGCACATAAATAAAGGTCAGATTCGGTTCCGAGAGATCGGGTGAAATCTGCGGGTTTAcc < 1:713221/65‑1 (MQ=255)
ccggcGGCACATAAATAAAGGTCAGATTCGGTTCCGAGAGATCGGGTGAAATCTGCGGGTTTAcc < 1:2268396/65‑1 (MQ=255)
ggcggcACATAAATAAAGGTCAGATTCGGTTCCGAGAGATCGGGTGAAATCTg < 1:1669680/53‑1 (MQ=255)
ggcggcACATAAATAAAGGTCAGATTCGGTTCCGAGAGATCGGGTGAAATCTg < 1:1354625/53‑1 (MQ=255)
ggcggcACATAAATAAAGGTCAGATTCGGTTCCGAGAGATCGGGTGAAATCTg < 1:355654/53‑1 (MQ=255)
ggcggcACATAAATAAAGGTCAGATTCGGTTCCGAGAGATCGGGTGAAATCTg < 1:312073/53‑1 (MQ=255)
ggcggcACATAAATAAAGGTCAGATTCGGTTCCGAGAGATCGGGTGAAATCTg < 1:2566778/53‑1 (MQ=255)
ggcggcACATAAATAAAGGTCAGATTCGGTTCCGAGAGATCGGGTGAAATCTg < 1:1013598/53‑1 (MQ=255)
cacaTAAATAAAGGTCAGATTCGGTTCCGAGAGATCGGGTGAAATCTGCGGGTTTACCAGCGTCACttt < 1:1644236/69‑1 (MQ=255)
cacaTAAATAAAGGTCAGATTCGGTTCCGAGAGATCGGGTGAAATCTGCGGGTTTACCAGCGTCACttt < 1:2060216/69‑1 (MQ=255)
|
ATCGACTCAATATTTGGCGCGCGGTTATACAGATACCAACCTGAACGGTTAGCCCGGCCCGGCGGCACATAAATAAAGGTCAGATTCGGTTCCGAGAGATCGGGTGAAATCTGCGGGTTTACCAGCGTCACTTT > minE/2406034‑2406167
|
| 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
