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 |
2,342,957 |
A→G |
43.3% |
L228L (CTA→CTG) |
glnL → |
sensory kinase in two‑component regulatory system with GlnG |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,342,957 | 0 | A | G | 43.3%
| 14.0
/ 51.2
| 67 | L228L (CTA→CTG) | glnL | sensory kinase in two‑component regulatory system with GlnG |
| Reads supporting (aligned to +/- strand): ref base A (15/23); new base G (7/22); total (22/45) |
| Fisher's exact test for biased strand distribution p-value = 2.03e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ACGCTGGTGTCGATGGAACTGCCGGACAACGTGCGGTTGATTCGTGATTACGATCCCAGCCTACCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAATATTGTGCGCAATGCGC > minE/2342895‑2343021
|
aCGCTGGTGTCGATGGAACTGCCGGACAACGTGCGGTTGATTCGTGATTACGATCCCAGCCTACCGGaa > 1:2274089/1‑69 (MQ=255)
aCGCTGGTGTCGATGGAACTGCCGGACAACGTGCGGTTGATTCGTGATTACGATCCCAGCCTACCGGaa > 1:1795378/1‑69 (MQ=255)
aCGCTGGTGTCGATGGAACTGCCGGACAACGTGCGGTTGATTCGTGATTACGATCCCAGCCTACCGGaa > 1:2698530/1‑69 (MQ=255)
aCGCTGGTGTCGATGGAACTGCCGGACAACGTGCGGTTGATTCGTGATTACGATCCCAGCCTACCGGaa > 1:2270199/1‑69 (MQ=255)
gATGGAACTGCCGGACAACGTGCGGTTGATTCGTGATTACGATCCCAGCCTACCGGAACTGGCGCACGa > 1:1284414/1‑69 (MQ=255)
gATGGAACTGCCGGACAACGTGCGGTTGATTCGTGATTACGATCCCAGCCTACCGGAACTGGCGCACGa < 1:2782090/69‑1 (MQ=255)
gATGGAACTGCCGGACAACGTGCGGTTGATTCGTGATTACGATCCCAGCCTACCGGAACTGGCGCACGa < 1:291740/69‑1 (MQ=255)
gATGGAACTGCCGGACAACGTGCGGTTGATTCGTGATTACGATCCCAGCCTACCGGAACTGGCGCACGa > 1:578797/1‑69 (MQ=255)
aTGGAACTGCCGGACAACGTGCGGTTGATTCGTGATTACGATCCCAGCCTACCGGAACTGGCGCACGa < 1:2379125/68‑1 (MQ=255)
gAAGTGCCGGACAACGTGCGGTTGATTCGTGATTAAGATCCCAGCCTACCGGa > 1:587286/1‑53 (MQ=255)
gAACTGCCGGACAACGTGCGGTTGATTCGTGATTACGATCCCAGCCTACCGGa > 1:725157/1‑53 (MQ=255)
gAACTGCCGGACAACGTGCGGTTGATTCGTGATTACGATCCCAGCCTACCGGa > 1:2924895/1‑53 (MQ=255)
gAACTGCCGGACAACGTGCGGTTGATTCGTGATTACGATCCCAGCCTACCGGa > 1:2046016/1‑53 (MQ=255)
aCTGCCGGACAACGTGCGGTTGATTCGTGATTACGATCCCAGCCTACCGGa < 1:400153/51‑1 (MQ=255)
gCCGGACAACGTGCGGTTGATTCGTGATTACGATCCCAGCCTACCGGAACTGGCGCACGACCCGGATCa < 1:638745/69‑1 (MQ=255)
gCCGGACAACGTGCGGTTGATTCGTGATTACGATCCCAGCCTACCGGAACTGGCGCACGACCCGGATCa < 1:1679110/69‑1 (MQ=255)
gCCGGACAACGTGCGGTTGATTCGTGATTACGATCCCAGCCTACCGGAACTGGCGCACGACCCGGATCa < 1:150300/69‑1 (MQ=255)
gCCGGACAACGTGCGGTTGATTCGTGATTACGATCCCAGCCTACCGGAACTGGCGCACGACCCGGATCa < 1:2862467/69‑1 (MQ=255)
aCAACGTGCGGTTGATTCGTGATTACGATCCCCGCCTACCGGAACTGGCGCACGACCCCGATCAAATTg < 1:1173817/69‑1 (MQ=255)
aCAACGTGCGGTTGATTCGTGATTACGATCCCAGCCTACCGGAACTGGCGCACGACCCGGATCAAATTg < 1:2877280/69‑1 (MQ=255)
aCAACGTGCGGTTGATTCGTGATTACGATCCCAGCCTACCGGAACTGGCGCACGACCCGGATCAAATTg < 1:540998/69‑1 (MQ=255)
aCAACGTGCGGTTGATTCGTGATTACGATCCCAGCCTACCGGAACTGGCGCACGACCCGGATCAAATTg < 1:3234438/69‑1 (MQ=255)
aCAACGTGCGGTTGATTCGTGATTACGATCCCAGCCTACCGGAACTGGCGCACGACCCGGATCAAATTg < 1:3303258/69‑1 (MQ=255)
aaCGTGCGGTT‑ATTCGTGATTACGATCCCAGCCTACCGGAACTGGCGCACGACCCGGATCAAATTGAAc < 1:1518654/69‑1 (MQ=255)
aCGTGCGGTTGATTCGTGATTACGATCCCAGCCTACCGGAACTGGCGCACGACCCGGATCAAATTGAAc < 1:1865905/69‑1 (MQ=255)
aCGTGCGGTTGATTCGTGATTACGATCCCAGCCTACCGGAACTGGCGCACGACCCGGATCAAATTGAAc < 1:588301/69‑1 (MQ=255)
gATTCGGGATTACGACCCCAGCCTGCCGGAACTGGCGCACGACCCGGATc > 1:203314/1‑50 (MQ=37)
gATTCGGGATTACGACCCCAGCCTGCCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGc > 1:2601149/1‑68 (MQ=39)
gATTCGGGATTACGACCCCAGCCTGCCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGc > 1:2680112/1‑68 (MQ=39)
gATTCGGGATTACGACCCCAGCCTGCCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGc > 1:1927026/1‑68 (MQ=39)
gATTCGGGATTACGACCCCAGCCTGCCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGc > 1:1789679/1‑68 (MQ=39)
gATTCGGGATTACGACCCCAGCCTGCCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGc > 1:711355/1‑68 (MQ=39)
gATTCGGGATTACGACCCCAGCCTGCCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGc > 1:951633/1‑68 (MQ=39)
cGTGATTACGATCCCAGCCTACCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGaa > 1:1374954/1‑68 (MQ=255)
cGTGATTACGATCCCAGCCTACCGGAACTGGCGCACGACCAGGATCAAATTGAACAGGTCTTGcag > 1:1163404/1‑64 (MQ=255)
tGATTACGATCCCAGCCTACCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAata < 1:1662084/68‑1 (MQ=255)
tGATTACGATCCCAGCCTACCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAata < 1:50291/68‑1 (MQ=255)
tGATTACGATCCCAGCCTACCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAata < 1:2092741/68‑1 (MQ=255)
tGATTACGATCCCAGCCTACCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAata < 1:3006337/68‑1 (MQ=255)
tGATTACGATCCCAGCCTACCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAata < 1:1613702/68‑1 (MQ=255)
tGATTACGATCCCAGCCTACCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAata < 1:2253093/68‑1 (MQ=255)
tGATTACGATCCCAGCCTACCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAata < 1:2788822/68‑1 (MQ=255)
gATTACGACCCCAGCCTGCCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAatat < 1:1577098/68‑1 (MQ=255)
gATTACGACCCCAGCCTGCCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAatat < 1:1421446/68‑1 (MQ=255)
gATTACGACCCCAGCCTGCCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAatat < 1:219469/68‑1 (MQ=255)
gATTACGACCCCAGCCTGCCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAatat < 1:2773135/68‑1 (MQ=255)
gATTACGACCCCAGCCTGCCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAatat < 1:3136979/68‑1 (MQ=255)
gATTACGACCCCAGCCTGCCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAatat < 1:167477/68‑1 (MQ=255)
gATTACGACCCCAGCCTGCCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAatat < 1:1904491/68‑1 (MQ=255)
gATTACGACCCCAGCCTGCCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAatat < 1:1779150/68‑1 (MQ=255)
gATTACGACCCCAGCCTGCCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAatat < 1:1800124/68‑1 (MQ=255)
gATTACGACCCCAGCCTGCCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAatat < 1:42925/68‑1 (MQ=255)
gATTACGACCCCAGCCTGCCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAatat < 1:2488490/68‑1 (MQ=255)
gATTACGACCCCAGCCTGCCGGAACTGGAGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAatat < 1:827836/68‑1 (MQ=255)
aCGATCCCAGCCTACCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAATATtgtg > 1:2388473/1‑68 (MQ=255)
aCGATCCCAGCCTACCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAATATtgtg > 1:541576/1‑68 (MQ=255)
aCGATCCCAGCCTACCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAATATtgtg > 1:3286091/1‑68 (MQ=255)
gCCTGCCGGAACTGGCGCACGACCCGGATCAAATTGACCAGGTCTTGCTGAATATTGTGCGCAATgcgc < 1:480013/69‑1 (MQ=255)
gCCTGCCGGAACTGGCGCACGACCCGGATCAAATTGAATAGGTCTTGCTGAATATTGTGCGCAATgcgc < 1:3361385/69‑1 (MQ=255)
gCCTGCCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAATATTGTGCGCAATgcgc < 1:3301997/69‑1 (MQ=255)
gCCTGCCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAATATTGTGCGCAATgcgc < 1:2887512/69‑1 (MQ=255)
gCCTGCCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAATATTGTGCGCAATgcgc < 1:2366967/69‑1 (MQ=255)
gCCTGCCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAATATTGTGCGCAATgcgc < 1:1504359/69‑1 (MQ=255)
gCCTGCCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAATATTGTGCGCAATgcgc < 1:2372892/69‑1 (MQ=255)
gCCTGCCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAATATTGTGCGCAATgcgc < 1:2378820/69‑1 (MQ=255)
gCCTGCCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAATATTGTGCGCAATgcgc < 1:1050575/69‑1 (MQ=255)
gCCTGCCGGAACTGACGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAATATTGTGCGCAATgcgc < 1:2149221/69‑1 (MQ=255)
|
ACGCTGGTGTCGATGGAACTGCCGGACAACGTGCGGTTGATTCGTGATTACGATCCCAGCCTACCGGAACTGGCGCACGACCCGGATCAAATTGAACAGGTCTTGCTGAATATTGTGCGCAATGCGC > minE/2342895‑2343021
|
| 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
