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 |
775,500 |
T→C |
35.2% |
L375L (TTA→CTA) ‡ |
icd → |
isocitrate dehydrogenase, specific for NADP+ |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 775,500 | 0 | T | C | 35.2%
| 51.6
/ 49.5
| 54 | L375L (TTA→CTA) ‡ | icd | isocitrate dehydrogenase, specific for NADP+ |
| Reads supporting (aligned to +/- strand): ref base T (12/23); new base C (12/7); total (24/30) |
| Fisher's exact test for biased strand distribution p-value = 5.06e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCT > minE/775430‑775564
|
aaaTCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACt > 1:1124496/1‑71 (MQ=255)
aaaTCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACt > 1:3263982/1‑71 (MQ=255)
ctctATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTa < 1:3803664/71‑1 (MQ=255)
tattatTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTaa < 1:3346182/69‑1 (MQ=255)
ctctcCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATgg < 1:1377093/70‑1 (MQ=255)
ctctcCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATgg < 1:3127539/70‑1 (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)
ctgAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTc > 1:226522/3‑71 (MQ=255)
ccGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTc < 1:3111728/71‑1 (MQ=255)
cGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTc > 1:1353041/1‑70 (MQ=255)
cGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCg < 1:2441030/71‑1 (MQ=255)
cGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCg < 1:587455/71‑1 (MQ=255)
aaGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCa < 1:1300231/42‑1 (MQ=255)
aaGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGaa > 1:583720/1‑70 (MQ=255)
aGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGc < 1:775697/71‑1 (MQ=255)
cGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTa < 1:378070/58‑1 (MQ=25)
gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt < 1:353651/71‑1 (MQ=255)
gCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAAct < 1:819651/54‑2 (MQ=25)
cTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCa < 1:456989/36‑1 (MQ=255)
tGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTa > 1:318741/1‑54 (MQ=21)
tGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTc > 1:3342495/1‑61 (MQ=25)
tGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTc < 1:1910208/68‑1 (MQ=255)
aCTTAATTGTTAAAGGTATGGAAGGCGCAATCAAcgc > 1:1044885/1‑37 (MQ=255)
aCTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGAGAAAAcc > 1:1837481/1‑44 (MQ=255)
|
AAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCT > minE/775430‑775564
|
| 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
