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 |
2,558,404 |
T→C |
66.8% |
V197V (GTT→GTC) |
gpsA → |
glycerol‑3‑phosphate dehydrogenase (NAD+) |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,558,404 | 0 | T | C | 66.8%
| 28.1
/ 17.5
| 39 | V197V (GTT→GTC) | gpsA | glycerol‑3‑phosphate dehydrogenase (NAD+) |
| Reads supporting (aligned to +/- strand): ref base T (8/5); new base C (14/12); total (22/17) |
| Fisher's exact test for biased strand distribution p-value = 7.40e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AAAAGTTTCCGCGTTTACAGCAATCCGGATTTCATTGGCGTGCAGCTTGGCGGCGCGGTGAAAAACGTTATTGCCATTGGTGCGGGGATGTCCGACGGTATCGGTTTTGGTGCG > minE/2558336‑2558449
|
aaaaGTTTCCGCGTTTACAGCAATCCGGATTTCATTGGCGTGCAGCTTGGCGGCGCGGTGAAAAACGtt < 1:2207007/69‑1 (MQ=255)
aaaaGTTTCCGCGTTTACAGCAATCCGGATTTCATTGGCGTGCAGCTTGGCGGCGCGGTGAAAAACGtt < 1:938418/69‑1 (MQ=255)
aaaaGTTTCCGCGTTTACAGCAATCCGGATTTCATTGGCGTGCAGCTTGGCGGCGCGGTGAAAAACGtt < 1:2529335/69‑1 (MQ=255)
aaaaGTTTCCGCGTTTACAGCAATCCGGATTTCATTGGCGTGCAGCTTGGCGGCGCGGTGAAAAACGtt < 1:3275057/69‑1 (MQ=255)
aaaaGTTTCCGCGTTTACAGCAATCCGGATTTCATTGGCGTGCAGCTTGGCGGCGCGGTGAAAAACGtt < 1:1770337/69‑1 (MQ=255)
aaaaGTTTCCGCGTTTACAGCAATCCGGATTTCATTGGCGTGCAGCTTGGCGGCGCGGTGAAAAACGtt < 1:1531845/69‑1 (MQ=255)
aaaaGTTTCCGCGTTTACAGCAATCCGGATTTCATTGGCGTGCAGCTTGGCGGCGCGGTGAAAAACGtt < 1:2718985/69‑1 (MQ=255)
aaaaGTTTCCGCGTTTACAGCAATCCGGATTTCATTGGCGTGCAGCTTGGCGGCGCGGTGAAAAACGtt < 1:2902691/69‑1 (MQ=255)
aaaaGTTTCCGCGTTTACAGCAATCCGGATTTCATTGGCGTGCAGCTTGGCGGCGCGGTGAAAAACGtt < 1:2898567/69‑1 (MQ=255)
aGTTTCCGCGTTTACAGCAATCCGGATTTCATTGGCGTGCAGCTTGGCGGCGCGGTGAAAAACGTTAtt > 1:726646/1‑69 (MQ=255)
tACAGCAATCCGGATTTCATTGGCGTGCAGCTTGGCGGCGCGGTGAAAAACGTTATTGCCATTGGTGCg > 1:1142503/1‑69 (MQ=255)
tACAGCAATCCGGATTTCATTGGCGTGCAGCTTGGCGGCGCGGTGAAAAACGTTATTGCCATTGGTGCg > 1:2285213/1‑69 (MQ=255)
tACAGCAATCCGGATTTCATTGGCGTGCAGCTTGGCGGCGCGGTGAAAAACGTTATTGCCATTGGTGCg > 1:3107881/1‑69 (MQ=255)
tACAGCAATCCGGATTTCATTGGCGTGCAGCTTGGCGGCGCGGTGAAAAACGTTATTGCCATTGGTGCg > 1:909745/1‑69 (MQ=255)
tACAGCAATCCGGATTTCATTGGCGTGCAGCTTGGCGGCGCGGTGAAAAACGTTATTGCCATTGGTGCg > 1:1006206/1‑69 (MQ=255)
aGCAATCCGGATTTCATTGGCGTGCAGCTTGGCGGCGCGGTGAAAAACGTTATTGCCATTGGTGCggg < 1:300722/68‑1 (MQ=255)
aGCAATCCGGATTTCATTGGCGTGCAGCTTGGCGGCGCGGTGAAAAACGTTATTGCCATTGGTGCggg < 1:2399783/68‑1 (MQ=255)
cGGATTTCATTGGCGTGCAGCTTGGCGGCGCGGTGAAAAACGTTATTGCCATTGGTGCGGGGATGTcc > 1:973697/1‑68 (MQ=255)
cGGATTTCATTGGCGTGCAGCTTGGCGGCGCGGTGAAAAACGTTATTGCCATTGGTGCGGGGATGTCCg > 1:169307/1‑69 (MQ=255)
cGGATTTCATCGGTGTGCAGCTTGGCGGTGCGGTGAAAAACGTCATTGCCATTGGCGCGGGGATGTCCg < 1:1168969/69‑1 (MQ=255)
cGGATTTCATCGGTGTGCAGCTTGGCGGTGCGGTGAAAAACGTCATTGCCATTGGCGCGGGGATGTCCg < 1:146161/69‑1 (MQ=255)
cGGATTTCATCGGTGTGCAGCTTGGCGGTGCGGTGAAAAACGTCATTGCCATTGGCGCGGGGATGTCCg < 1:2132274/69‑1 (MQ=255)
cGGATTTCATCGGTGTGCAGCTTGGCGGTGCGGTGAAAAACGTCATTGCCATTGGCGCGGGGATGTCCg < 1:276753/69‑1 (MQ=255)
cGGATTTCATCGGTGTGCAGCTTGGCGGTGCGGTGAAAAACGTCATTGCCATTGGCGCGGGGATGTCCg < 1:51249/69‑1 (MQ=255)
cGGATTTCATCGGTGTGCAGCTTGGCGGTGCGGTGAAAAACGTCATTGCCATTGGCGCGGGGATGTCCg < 1:268259/69‑1 (MQ=255)
cGGATTTCATCGGTGTGCAGCTTGGCGGTGCGGTGAAAAACGTCATTGCCATTGGCGCGGGGATGTCCg < 1:2674745/69‑1 (MQ=255)
cGGATTTCATCGGTGTGCAGCTTGGCGGTGCGGTGAAAAACGTCATTGCCATTGGCGCGGGGATGTCCg < 1:783754/69‑1 (MQ=255)
cGGATTTCATCGGTGTGCAGCTTGGCGGTGCGGTGAAAAACGTCATTGCCATTGGCGCGGGGATGTCCg < 1:859027/69‑1 (MQ=255)
cGGATTTCATCGGTGTGCAGCTTGGCGGTGCGGTGAAAAACGTCATTGCCATTGGCGCGGGGATGTCCg < 1:2076349/69‑1 (MQ=255)
cGGATTTCATCGGTGTGCAGCTTGGCGGTGCGGTGAAAAACGTCATTGCCATTGGCGCGGGGATGTCCg < 1:2077693/69‑1 (MQ=255)
cGGATTTCATCGGTGTGCAGATTGGCGGTGCGGTGAAAAACGTCATTGCCATTGGCGCGGGGATGTCCg < 1:1235502/69‑1 (MQ=255)
cTTGGCGGCGCGGTGAAAAACGTTATTGCCATTGGTGCGGGGATGTCCGACGGTATCGGTTTTGGTGCg < 1:662853/69‑1 (MQ=255)
tGGCGGCGCGTTGAAAAACGTTATTGCCATTGGTGCggg < 1:2438418/39‑1 (MQ=255)
tGGCGGCGCGGTGAAAAACGTTATTGCCATTGGTGCGGGGATGTCCGACGGTATCGGTTTTGGTGCg < 1:34887/67‑1 (MQ=255)
aaaaCGTCATTGGCATTGGCGCGGGGATGTCCGACGGTATCGGTTTTg > 1:1652191/1‑48 (MQ=255)
aaaaCGTCATTGCCATTGGCGCGGGGATGTCCGACGGTATGGGTTTTg > 1:1795249/1‑48 (MQ=38)
aaaaCGTCATTGCCATTGGCGCGGGGATGTCCGACGGTATCgg > 1:3326106/1‑43 (MQ=38)
aaaaCGTCATTGCCATTGGCGCGGGGATGTCCGACGGTATCGGTTTTg > 1:3111683/1‑48 (MQ=39)
aaaaCGTCATTGCCATTGGCGCGGGGATGTCCGACGGTATCGGTTTTg > 1:3139948/1‑48 (MQ=39)
aaaaCGTCATTGCCATTGGCGCGGGGATGTCCGACGGTATCGGTTTTg > 1:1389854/1‑48 (MQ=39)
aaaaCGTCATTGCCATTGGCGCGGGGATGTCCGACGGTATCGGTTTTg > 1:1697609/1‑48 (MQ=39)
aaaaCGTCATTGCCATTGGCGCGGGGATGTCCGACGGTATCGGTTTTg > 1:1752983/1‑48 (MQ=39)
aaaaCGTCATTGCCATTGGCGCGGGGATGTCCGACGGTATCGGTTTTg > 1:2615569/1‑48 (MQ=39)
aaaaCGTCATTGCCATTGGCGCGGGGATGTCCGACGGTATCGGTTTTg > 1:261481/1‑48 (MQ=39)
aaaaCGTCATTGCCATTGGCGCGGGGATGTCCGACGGTATCGGTTTTg > 1:2547126/1‑48 (MQ=39)
aaaaCGTCATTGCCATTGGCGCGGGGATGTCCGACGGTATCGGTTTTg > 1:1218836/1‑48 (MQ=39)
aaaaCGTCATTGCCATTGGCGCGGGGATGTCCGACGGTATCGGTTTTg > 1:1205480/1‑48 (MQ=39)
aaaaCGTCATTGCCATTGGCGCGGGGATGTCCGACGGTATCGGTTTTg > 1:2216837/1‑48 (MQ=39)
|
AAAAGTTTCCGCGTTTACAGCAATCCGGATTTCATTGGCGTGCAGCTTGGCGGCGCGGTGAAAAACGTTATTGCCATTGGTGCGGGGATGTCCGACGGTATCGGTTTTGGTGCG > minE/2558336‑2558449
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
