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 |
2,905,236 |
A→T |
42.1% |
G286G (GGT→GGA) |
treC ← |
trehalose‑6‑P hydrolase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,905,236 | 0 | A | T | 42.1%
| 20.1
/ 56.7
| 57 | G286G (GGT→GGA) | treC | trehalose‑6‑P hydrolase |
| Reads supporting (aligned to +/- strand): ref base A (10/23); new base T (5/19); total (15/42) |
| Fisher's exact test for biased strand distribution p-value = 5.47e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.79e-01 |
GCCAGTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCACCGGGATAATCGACCTTCAGGTGATGAAAATTAAAGGTCATCGACAATTCACTGCCTGTCAGAGCCG > minE/2905172‑2905303
|
gCCAGTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCACCgg < 1:2265868/69‑1 (MQ=255)
aGTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCACCGGGAt < 1:1962346/69‑1 (MQ=255)
aGTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCACCGGGAt < 1:3014617/69‑1 (MQ=255)
aGTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCACCGGGAt < 1:2822974/69‑1 (MQ=255)
aGTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCACCGGGAt < 1:3169358/69‑1 (MQ=255)
aGTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCACCGGGAt < 1:2474106/69‑1 (MQ=255)
aGTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCACCGGGAt < 1:2344781/69‑1 (MQ=255)
aGTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCACCGGGAt < 1:1941674/69‑1 (MQ=255)
aGTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCACCGGGAt < 1:190229/69‑1 (MQ=255)
aGTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCACCGGGAt < 1:426126/69‑1 (MQ=255)
aGTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCACCGGGAt < 1:163983/69‑1 (MQ=255)
gTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCTCCGGGATa < 1:146872/69‑1 (MQ=255)
gTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCTCCGGGATa < 1:1118495/69‑1 (MQ=255)
gTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCTCCGGGATa < 1:2939159/69‑1 (MQ=255)
gTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCTCCGGGATa < 1:866093/69‑1 (MQ=255)
gTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCTCCGGGATa < 1:2656454/69‑1 (MQ=255)
gTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCTCCGGGATa < 1:1129659/69‑1 (MQ=255)
gTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCTCCGGGATa < 1:2421652/69‑1 (MQ=255)
gTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCTCCGGGATa < 1:697398/69‑1 (MQ=255)
gTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCTCCGGGATa < 1:3257254/69‑1 (MQ=255)
gTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCTCCGGGATa < 1:119923/69‑1 (MQ=255)
gTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCTCCGGGATa < 1:3415111/69‑1 (MQ=255)
gTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCTCCGGGATa < 1:2105919/69‑1 (MQ=255)
gTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCTCCGGGATa < 1:663268/69‑1 (MQ=255)
gTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCTCCGGGATa < 1:437842/69‑1 (MQ=255)
gTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCTCCGGGATa < 1:1985916/69‑1 (MQ=255)
gTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCTCCGGGATa < 1:123909/69‑1 (MQ=255)
gTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCTCCGGGATa < 1:1726826/69‑1 (MQ=255)
gTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCTCCGGGATa < 1:1404116/69‑1 (MQ=255)
cGGAACAATGTTTTCAACTCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCACCGTGAt < 1:292613/64‑1 (MQ=255)
cAATGTTTTCAACGCCACAAAGTCAGGTTTATCCAGCGTCCATTTTTCACCTCCGGGATa < 1:419323/60‑1 (MQ=39)
tGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCACCGGGATa > 1:135471/1‑57 (MQ=255)
ttCACCGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCTCCGGGATAATCGACCTTCAgg > 1:3285478/1‑66 (MQ=255)
ttCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCTCCGGGATAATCGACCTTCAGGtg > 1:11622/1‑68 (MQ=255)
ttCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCTCCGGGATAATCGACCTTCAGGtg > 1:3125289/1‑68 (MQ=255)
ttCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCTCCGGGATAATCGACCTTCAGGtg > 1:1757272/1‑68 (MQ=255)
ttCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCTCCGGGATAATCGACCTTCAGGtg > 1:3405445/1‑68 (MQ=255)
cGCCACAAAGTCAGGTTTAGCCATCGTCCATTTTTCACCACCGGGATAATCGACCTTCAGGTGATGaa < 1:3217588/68‑1 (MQ=255)
cGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCACCGGGATAATCGACCTTCAGGTGATGaa < 1:922317/68‑1 (MQ=255)
cGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCACCGGGATAATCGACCTTCAGGTGATGaa < 1:2425957/68‑1 (MQ=255)
acaAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCACCGGGATAATCGACCTTCAGGTGATGAAAATTa < 1:2617667/69‑1 (MQ=255)
acaAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCACCGGGATAATCGACCTTCAGGTGATGAAAATTa < 1:3387098/69‑1 (MQ=255)
acaAAGTCAGGTTTACCCAGCGTCCATTTTTCACCACCGGGATAATCGACCTTCAGGTGATGAAAATTa < 1:2320089/69‑1 (MQ=255)
ttAGCCAGCGTCCATTTTTCACCACCGGGATAATc > 1:2538167/1‑35 (MQ=255)
ttAGCCAGCGTCCATTTTTCACCACCGGGATAATc > 1:207923/1‑35 (MQ=255)
gCCAGCGTCCATTTTTCACCACCGGGATAATCGACCTTCAGGTGATGAAAATTAAAGGTCATCGACaa < 1:3379328/68‑1 (MQ=255)
gCCAGCGTCCATTTTTCACCACCGGGATAATCGACCTTCAGGTGATGAAAATTAAAGGTCATCGACaa < 1:715313/68‑1 (MQ=255)
gCCAGCGTCCATTTTTCACCACCGGGATAATCGACCTTCAGGTGATGAAAATTAAAGGTCATCGACaa < 1:1175890/68‑1 (MQ=255)
cAGCGTCCATTTTTCACCACCGGGATAATCGACCTTCAGGTGATGAAAATTAAAGGTCATCGACAATTc < 1:2109046/69‑1 (MQ=255)
cAGCGTCCATTTTTCACCACCGGGATAATCGACCTTCAGGTGATGAAAATTAAAGGTCATCGACAATTc < 1:1120707/69‑1 (MQ=255)
cATTTTTCACCACCGGGTTAATCGACCTTCAGGTGATGAAAATTAAAGGTCATCGACaa > 1:2225185/1‑59 (MQ=255)
cATTTTTCACCACCGGGATAATCGACCTTCAGGTGATGAAAATTAAAGGTCATCGACAATTCACTGCCt > 1:1883338/1‑69 (MQ=255)
cATTTTTCACCACCGGGATAATCGACCTTCAGGTGATGAAAATTAAAGGTCATCGACAATTCACTGCCt > 1:1611828/1‑69 (MQ=255)
cATTTTTCACCACCGGGATAATCGACCTTCAGGTGATGAAAATTAAAGGTCATCGACAATTCACTGCCt > 1:2987482/1‑69 (MQ=255)
cATTTTTCACCACCGGGATAATCGACCTTCAGGTGATGAAAATTAAAGGTCATCGACAATTCACTGCCt > 1:2259437/1‑69 (MQ=255)
cATTTTTCACCACCGGGATAATCGACCTTCAGGTGATGAAAATTAAAGGTCATCGACAATTCACTGCCt > 1:903354/1‑69 (MQ=255)
cATTTTTCACCACCGGGATAATCGACCTTCAGGTGATGAAAATTAAAGGTCATCGACAATTCACTGCCt > 1:1119468/1‑69 (MQ=255)
caccGGGATAATCGACCTTCAGGTGATGAAAATTAAAGGTCATCGACAATTCACTGCCTGTCAGAGCcg < 1:1721660/69‑1 (MQ=255)
|
GCCAGTGGCGGAACAATGTTTTCAACGCCACAAAGTCAGGTTTAGCCAGCGTCCATTTTTCACCACCGGGATAATCGACCTTCAGGTGATGAAAATTAAAGGTCATCGACAATTCACTGCCTGTCAGAGCCG > minE/2905172‑2905303
|
| 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
