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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
775,487 |
C→T |
24.5% |
T370T (ACC→ACT) |
icd → |
isocitrate dehydrogenase, specific for NADP+ |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 775,487 | 0 | C | T | 24.5%
| 85.6
/ 25.7
| 49 | T370T (ACC→ACT) | icd | isocitrate dehydrogenase, specific for NADP+ |
| Reads supporting (aligned to +/- strand): ref base C (16/21); new base T (8/4); total (24/25) |
| Fisher's exact test for biased strand distribution p-value = 1.96e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCG > minE/775417‑775557
|
gTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGAcc < 1:2267106/71‑1 (MQ=255)
gTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGAcc > 1:3802079/1‑71 (MQ=255)
gTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGAcc > 1:3059513/1‑71 (MQ=255)
tCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTCCGCCACATGGGTTGGACCg < 1:2033961/71‑1 (MQ=255)
ggACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAg < 1:2203892/71‑1 (MQ=255)
aCAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCg < 1:1138752/71‑1 (MQ=255)
cAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCgg > 1:714894/1‑71 (MQ=255)
cAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCg > 1:2753179/1‑70 (MQ=255)
aaaGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGc < 1:1649686/71‑1 (MQ=255)
aaaTCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACt > 1:3263982/1‑71 (MQ=255)
aaaTCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACt > 1:1124496/1‑71 (MQ=255)
cTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTg < 1:777707/63‑1 (MQ=255)
ctctATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTa < 1:3803664/71‑1 (MQ=255)
tattatTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTaa < 1:3346182/69‑1 (MQ=255)
ttattCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAg > 1:1626294/1‑48 (MQ=255)
ttattCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAg > 1:1041134/1‑48 (MQ=255)
ctctcCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATgg < 1:1377093/70‑1 (MQ=255)
ctctcCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATgg < 1:3127539/70‑1 (MQ=255)
tcCGCTGAGATGATGCTGCGCCACATGTGTTGGACCGAAg > 1:607895/1‑40 (MQ=255)
tcCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGa < 1:1239885/68‑1 (MQ=255)
tcCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGa < 1:1499814/68‑1 (MQ=255)
cGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAg < 1:2283565/68‑1 (MQ=255)
cGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGgcg > 1:3301351/1‑71 (MQ=255)
cTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATgg > 1:1714068/1‑63 (MQ=255)
tGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCaa > 1:3162991/1‑71 (MQ=255)
gatgatGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCa < 1:2997594/71‑1 (MQ=255)
gacgatgCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCa < 1:2011454/68‑1 (MQ=255)
ctaatgCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCaa < 1:3770846/68‑1 (MQ=255)
atgatgCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCaa < 1:1334831/71‑1 (MQ=255)
tgatgCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCaa < 1:164725/70‑1 (MQ=255)
gatgCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTaa < 1:3803803/48‑1 (MQ=255)
tgctgcGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTa > 1:2101086/1‑45 (MQ=255)
tgctgcGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAAtgcc < 1:2660882/71‑2 (MQ=255)
tgctgcGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAAtgc > 1:1458380/1‑70 (MQ=255)
tgctgcGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAAtgc > 1:3095905/1‑70 (MQ=255)
ctgcGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGaa < 1:236511/54‑1 (MQ=255)
cgcCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATgg > 1:339422/1‑49 (MQ=37)
cgcCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAg > 1:352914/1‑43 (MQ=255)
gcCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAAc > 1:3032286/1‑62 (MQ=255)
acaTGGGTTGGACCGAAGCGGCTGACTTAATTGTTaaa < 1:3699681/38‑1 (MQ=255)
caTGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTaa > 1:890819/1‑71 (MQ=255)
aTGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGTTATGGAAGGCGCAATCAATGCCAAGACCGTAAc > 1:2453484/1‑71 (MQ=255)
aTGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAAc > 1:841539/1‑71 (MQ=255)
tGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCaa > 1:248786/1‑55 (MQ=255)
gggTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAAct > 1:2044335/1‑69 (MQ=255)
gggTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCaa > 1:2328811/1‑54 (MQ=255)
gggTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAAc > 1:3033035/1‑69 (MQ=255)
ggTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAActt < 1:1609592/70‑3 (MQ=255)
ttGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATg < 1:2920408/71‑1 (MQ=255)
tGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGa > 1:889719/1‑71 (MQ=255)
gACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAg < 1:2726767/38‑1 (MQ=255)
gACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACt < 1:1054709/71‑1 (MQ=255)
ccGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTc < 1:3111728/71‑1 (MQ=255)
cGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTc > 1:1353041/1‑70 (MQ=255)
cGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCg < 1:587455/71‑1 (MQ=255)
cGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCg < 1:2441030/71‑1 (MQ=255)
|
GTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCG > minE/775417‑775557
|
| 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
