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 |
2,613,717 |
A→T |
67.4% |
L168L (CTT→CTA) |
acpT ← |
holo‑(acyl carrier protein) synthase 2 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,613,717 | 0 | A | T | 67.4%
| 47.7
/ 33.8
| 49 | L168L (CTT→CTA) | acpT | holo‑(acyl carrier protein) synthase 2 |
| Reads supporting (aligned to +/- strand): ref base A (12/4); new base T (17/16); total (29/20) |
| Fisher's exact test for biased strand distribution p-value = 1.36e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.43e-01 |
GCACACTGTCGGCGGTGAGCGTAAAGGGAGTAGGGGTGCAGATCGCAAGGCTTAAATTTTCAAGCTGACAATGGCTGACTGACAGCGAGGAGTGATAGGTGCTGTCTACGCTGACGATTT > minE/2613656‑2613775
|
gCACACTGTCGGCGGTGAGCGTAAAGGGAGTAGGGGTGCAGATCGCAAGGCTTAAATTTTCAAGCTGAc < 1:1407973/69‑1 (MQ=255)
ggcggTGAGCGTAAAGGGAGTAGGGGTGCAGATCGCAAGGCTTAAATTTTCAAGCTGACAATGGctgac > 1:1450313/1‑69 (MQ=255)
ggcggTGAGCGTAAAGGGAGTAGGGGTGCAGATCGCAAGGCTTAAATTTTCAAGCTGACAATGGctga > 1:3292345/1‑68 (MQ=255)
ggcggTGAGCGTAAAGGGAGTAGGGGTGCAGATCGCAAGGCTTAAATTTTCAAGCTGACAATGGctga > 1:584077/1‑68 (MQ=255)
ggcggTGAGCGTAAAGGGAGTAGGGGTGCAGATCGCAAGGCTTAAATTTTCAAGCTGACAATGGctga > 1:1870176/1‑68 (MQ=255)
gTGCAGATCGCCAGGCTTAAATTTTCTAGCTGACAATGGCTGACTGACAGCGATGAGTTAt < 1:873234/61‑1 (MQ=255)
gTGCAGATCGCCAGGCTTAAATTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTAt < 1:243486/61‑1 (MQ=255)
gTGCAGATCGCCAGGCTTAAATTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTAt < 1:554677/61‑1 (MQ=255)
gTGCAGATCGCCAGGCTTAAATTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTAt < 1:2514335/61‑1 (MQ=255)
gTGCAGATCGCCAGGCTTAAATTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTAt < 1:543717/61‑1 (MQ=255)
gTGCAGATCGCCAGGCTTAAATTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTAt < 1:1878000/61‑1 (MQ=255)
gTGCAGATCGCCAGGCTTAAATTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTAt < 1:737426/61‑1 (MQ=255)
gTGCAGATCGCCAGGCTTAAATTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTAt < 1:1686133/61‑1 (MQ=255)
gTGCAGATCGCCAGGCTTAAATTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTAt < 1:165484/61‑1 (MQ=255)
gTGCAGATCGCCAGGCTTAAATTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTAt < 1:2784553/61‑1 (MQ=255)
gTGCAGATCGCCAGGCTTAAATTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTAt < 1:767860/61‑1 (MQ=255)
gTGCAGATCGCCAGGCTTAAATTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTAt < 1:411761/61‑1 (MQ=255)
gTGCAGATCGCCAGGCTTAAATTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTAt < 1:2942131/61‑1 (MQ=255)
gTGCAGATCGCCAGGCTTAAATTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTAt < 1:3329023/61‑1 (MQ=255)
gTGCAGATCGCCAGGCTTAAATTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTAt < 1:3221201/61‑1 (MQ=255)
tCGCAAGGCTTAAATTTTCAAGCTGACAATGGCTGACTGACAGCGAGGAGTGa < 1:2690050/53‑1 (MQ=255)
tCGCAAGGCTTAAATTTTCAAGCTGACAATGGCTGACTGACAGCGAGGAGTGa < 1:2081500/53‑1 (MQ=255)
tCGCAAGGCTTAAATTTTCAAGCTGACAATGGCTGACTGACAGCGAGGAGTGa < 1:1393184/53‑1 (MQ=255)
cGCAAGGCTTAAATTTTCAAGCTGACAATGGCTGACTGACAGCGAGGAGTGATAGGTGCTGTCTACGCt > 1:2288252/1‑69 (MQ=255)
cGCAAGGCTTAAATTTTCAAGCTGACAATGGCTGACTGACAGCGAGGAGTGATAGGTGCTGTCTACGCt > 1:818802/1‑69 (MQ=255)
cGCAAGGCTTAAATTTTCAAGCTGACAATGGCTGACTGACAGCGAGGAGTGATAGGTGCTGTCTACGCt > 1:1170432/1‑69 (MQ=255)
cGCAAGGCTTAAATTTTCAAGCTGACAATGGCTGACTGACAGCGAGGAGTGATAGGTGCTGTCTACGCt > 1:3259192/1‑69 (MQ=255)
gCTTAAATTTTCAAGCTGACAATGGCTGACTGACAGCGAGGAGTGATAGGTGCTGTCTACGCTGACGAt > 1:431886/1‑69 (MQ=255)
gCTTAAATTTTCAAGCTGACAATGGCTGACTGACAGCGAGGAGTGATAGGTGCTGTCTACGCTGACGAt > 1:1007216/1‑69 (MQ=255)
cTTAAATTTTCAAGCTGACAATGGCTGACTGACAGCGAGGAGTGATAGGTGCTGTCTACGCTGACGAtt > 1:1963073/1‑69 (MQ=255)
cTTAAATTTTCAAGCTGACAATGGCTGACTGACAGCGAGGAGTGATAGGTGCTGTCTACGCTGACGAtt > 1:1506480/1‑69 (MQ=255)
aaaTTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTATAGGTGCTGTCTACGCTGACGAttt > 1:634831/1‑67 (MQ=255)
aaaTTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTATAGGTGCTGTCTACGCTGACGAttt > 1:975973/1‑67 (MQ=255)
aaaTTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTATAGGTGCTGTCTACGCTGACGAttt > 1:3344430/1‑67 (MQ=255)
aaaTTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTATAGGTGCTGTCTACGCTGACGAttt > 1:831429/1‑67 (MQ=255)
aaaTTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTATAGGTGCTGTCTACGCTGACGAttt > 1:3100770/1‑67 (MQ=255)
aaaTTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTATAGGTGCTGTCTACGCTGACGAttt > 1:3005810/1‑67 (MQ=255)
aaaTTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTATAGGTGCTGTCTACGCTGACGAttt > 1:2854121/1‑67 (MQ=255)
aaaTTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTATAGGTGCTGTCTACGCTGACGAttt > 1:2839694/1‑67 (MQ=255)
aaaTTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTATAGGTGCTGTCTACGCTGACGAttt > 1:275996/1‑67 (MQ=255)
aaaTTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTATAGGTGCTGTCTACGCTGACGAttt > 1:2274556/1‑67 (MQ=255)
aaaTTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTATAGGTGCTGTCTACGCTGACGAttt > 1:2168807/1‑67 (MQ=255)
aaaTTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTATAGGTGCTGTCTACGCTGACGAttt > 1:1769591/1‑67 (MQ=255)
aaaTTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTATAGGTGCTGTCTACGCTGACGAttt > 1:1430063/1‑67 (MQ=255)
aaaTTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTATAGGTGCTGTCTACGCTGACGAttt > 1:1337807/1‑67 (MQ=255)
aaaTTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTATAGGTGCTGTCTACGCTGACGAttt > 1:13001/1‑67 (MQ=255)
aaaTTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTATAGGTGCTGTCTACGCTGACGAttt > 1:1143681/1‑67 (MQ=255)
aaaTTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTATAGGTGCTGTCTACGCTGACGAttt > 1:1079986/1‑67 (MQ=255)
aTTTTCTAGCTGACAATGGCTGACTGACAGCGAGGAGTTAt < 1:2164811/41‑1 (MQ=255)
|
GCACACTGTCGGCGGTGAGCGTAAAGGGAGTAGGGGTGCAGATCGCAAGGCTTAAATTTTCAAGCTGACAATGGCTGACTGACAGCGAGGAGTGATAGGTGCTGTCTACGCTGACGATTT > minE/2613656‑2613775
|
| 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
