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 |
2,727,775 |
C→T |
35.3% |
S4S (TCC→TCT) |
kefB → |
potassium:proton antiporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,727,775 | 0 | C | T | 35.3%
| 30.3
/ 26.0
| 48 | S4S (TCC→TCT) | kefB | potassium:proton antiporter |
| Reads supporting (aligned to +/- strand): ref base C (16/15); new base T (12/5); total (28/20) |
| Fisher's exact test for biased strand distribution p-value = 2.36e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AGAGCCTACGGTGACTGGCTGGCAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCCGATTTTTTACTCGCAGGAGTGCTGTTTCTCTTCGCGGCGGTGGCTGCGGTGCCGCTGGCATCGC > minE/2727714‑2727839
|
agagCCTACGGTGACTGGCTGGCAAATCCGCTGTCTCCAGGGGGCCGCTGATGGAAGGTTCTGAtttt > 1:3000969/1‑68 (MQ=255)
agagCCTACGGTGACTGGCTGGCAAATCCGCTGTCTCCAGGGGGCCGCTGATGGAAGGTTCTGAtttt > 1:3004792/1‑68 (MQ=255)
agagCCTACGGTGACTGGCTGGCAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCTGAtttt > 1:2603941/1‑68 (MQ=255)
agagCCTACGGTGACTGGCTGGCAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCTGAtttt > 1:2399920/1‑68 (MQ=255)
agagCCTACGGTGACTGGCTGGCAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCTGAtttt > 1:1374712/1‑68 (MQ=255)
agagCCTACGGTGACTGGCTGGCAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCTGAtttt > 1:3187926/1‑68 (MQ=255)
agagCCTACGGTGACTGGCTGGCAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCTGAtttt > 1:54103/1‑68 (MQ=255)
agagCCTACGGTGACTGGCTGGCAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCTGAtttt > 1:517045/1‑68 (MQ=255)
agagCCTACGGTGACTGGCTGGCAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCTGAtttt > 1:1559625/1‑68 (MQ=255)
agagCCTACGGTGACTGGCTGGCAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCTGAtttt > 1:34796/1‑68 (MQ=255)
agagCCTACGGTGACTGGCTGGCAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCTGAttt > 1:879343/1‑67 (MQ=255)
agagCCTACGGTGACTGGCTGGCAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCTGAttt > 1:80468/1‑67 (MQ=255)
aCGGTGACTGGCTGGCAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCCGATTTTTTACTCGc < 1:301575/69‑1 (MQ=255)
aCGGTGACTGGCTGGCAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCCGATTTTTTACTCGc < 1:2086452/69‑1 (MQ=255)
aCGGTGACTGGCTGGCAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCCGATTTTTTACTCGc < 1:2667010/69‑1 (MQ=255)
gTGACTGGCTGGCAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCCGATTTTTTACTCGCAgg < 1:721126/69‑1 (MQ=255)
gTGACTGGCTGGCAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCCGATTTTTTACTCGCAgg < 1:2939528/69‑1 (MQ=255)
aCTGGCTGGCAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCCGATTTTTTACTCGCAGGAg > 1:226756/1‑68 (MQ=255)
aCTGGCTGGCAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCCGATTTTTTACTCGCAGGAGt > 1:1880465/1‑69 (MQ=255)
aCTGGCTGGCAAATCCGCTGTCTCCAGGAGGCCG‑‑GATGGAAGGTTCCGATTTTTTACTCGCAGGAGTGc > 1:2201180/1‑69 (MQ=255)
tggctggcAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCCGATTTTTTACTCGCAGGAGTg < 1:581301/68‑1 (MQ=255)
tggctggcAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCCGATTTTTTACTCGCAGGAGTg < 1:789750/68‑1 (MQ=255)
tggctggcAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCCGATTTTTTACTCGCAGGAGTg < 1:279834/68‑1 (MQ=255)
tggctggcAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCCGATTTTTTACTCGCAGGAGTg < 1:1140586/68‑1 (MQ=255)
tggctggcAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCCGATTTTTTACTCGCAGGAGTg < 1:1813119/68‑1 (MQ=255)
tggctggcAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCCGATTTTTTACTCGCAGGAGTg < 1:1408363/68‑1 (MQ=255)
tggctggcAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCCGATTTTTTACTCGCAGGAGTg < 1:1440563/68‑1 (MQ=255)
tggctggcAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCCGATTTTTTACTCGCAGGAGTg < 1:2062500/68‑1 (MQ=255)
cAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCCGATTTTTTACTCGCAGGAGTGCTGTTtct > 1:2258559/1‑69 (MQ=255)
cAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCCGATTTTTTACTCGCAGGAGTGCTGTTtct > 1:2648025/1‑69 (MQ=255)
cAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCCGATTTTTTACTCGCAGGAGTGCTGTTtct > 1:3005453/1‑69 (MQ=255)
cAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCCGATTTTTTACTCGCAGGAGTGCTGTTtct > 1:1374786/1‑69 (MQ=255)
aaaTCCGTTGTCTCCAGGAGGCCGCTGATGGAAGGTTCTGATTTTTTACTCGCAGGAGTGCTGTTtct < 1:2662815/68‑1 (MQ=255)
aaaTCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCTGATTTTTTACTCGCAGGAGTGCTGTTtct < 1:2169298/68‑1 (MQ=255)
aaaTCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCTGATTTTTTACTCGCAGGAGTGCTGTTtct < 1:1758783/68‑1 (MQ=255)
aaaTCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCTGATTTTTTACTCGCAGGAGTGCTGTTtct < 1:1284417/68‑1 (MQ=255)
aaTCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCTGATTTTTTACTCGCAGGAGTGCTGTTtct < 1:3130958/67‑1 (MQ=255)
aaTCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCCGATTTTTTACTCGCAGGAGTGCTGTTTctct > 1:635361/1‑69 (MQ=255)
gCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCCGATTTTTTACTCGCAGGAGTg < 1:1171901/54‑1 (MQ=255)
ggAAGGTTCCGATTTTTTACTCGCAGGAGTGCTGTTTCTCTTCGCGGCGGTGGCTGCGGTGCCGCTgg < 1:1610957/68‑1 (MQ=255)
gTTCCGATTTTTTACTCGCAGGAGTGCTGTTTCTCTTCGCGGCGGTGGCTGCGGTGCCGCTGGCATcgc > 1:2088395/1‑69 (MQ=255)
gTTCCGATTTTTTACTCGCAGGAGTGCTGTTTCTCTTCGCGGCGGTGGCTGCGGTGCCGCTGGCATcgc > 1:2552533/1‑69 (MQ=255)
gTTCCGATTTTTTACTCGCAGGAGTGCTGTTTCTCTTCGCGGCGGTGGCTGCGGTGCCGCTGGCATcg > 1:1069343/1‑68 (MQ=255)
gTTCCGATTTTTTACTCGCAGGAGTGCTGTTTCTCTTCGCGGCGGTGGCTGCGGTGCCGCTGGCATcg > 1:520875/1‑68 (MQ=255)
gTTCCGATTTTTTACTCGCAGGAGTGCTGTTTCTCTTCGCGGCGGTGGCTGCGGTGCCGCTGGCATcg > 1:1478586/1‑68 (MQ=255)
gTTCCGATTTTTTACTCGCAGGAGTGCTGTTTCTCTTCGCGGCGGTGGCTGCGGTGCCGCTGGCATcg > 1:3243893/1‑68 (MQ=255)
gTTCCGATTTTTTACTCGCAGGAGTGCTGTTTCTCTTCGCGGCGGTGGCTGCGGTGCCGCTGGCATcg > 1:274526/1‑68 (MQ=255)
gTTCCGATTTTTTACTCGCAGGAGTCCTGTTTCTCTTCGCGGCGGTGGCTGCGGTGCCGCTGGCATcgc > 1:3198866/1‑69 (MQ=255)
|
AGAGCCTACGGTGACTGGCTGGCAAATCCGCTGTCTCCAGGAGGCCGCTGATGGAAGGTTCCGATTTTTTACTCGCAGGAGTGCTGTTTCTCTTCGCGGCGGTGGCTGCGGTGCCGCTGGCATCGC > minE/2727714‑2727839
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
