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 |
1,527,855 |
G→A |
100% |
S280S (TCG→TCA) |
trmC → |
fused 5‑methylaminomethyl‑2‑thiouridine forming enzyme methyltransferase and FAD‑dependent demodification enzyme |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,527,855 | 0 | G | A | 76.2%
| 53.5
/ 12.9
| 46 | S280S (TCG→TCA) | trmC | fused 5‑methylaminomethyl‑2‑thiouridine forming enzyme methyltransferase and FAD‑dependent demodification enzyme |
| Reads supporting (aligned to +/- strand): ref base G (1/10); new base A (34/1); total (35/11) |
| Fisher's exact test for biased strand distribution p-value = 2.89e-08 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CACGGGCAGCAGCAAACGGGAAGCGGCGATTATCGGCGGTGGTATTGCCAGCGCGTTGTTGTCGCTGGCGCTATTACGGCGCGGCTGGCAGGTAACGCTTTATTGCGCGGATGAGGCCCCCGCACT > minE/1527792‑1527917
|
tatgggCAGCAACAAACAGGAAGCGGCAATTATTGGAGGCGGTATTGCCAGCGCGTTGTTGTCACTgg < 1:2390052/65‑1 (MQ=255)
gggCAGCAGCAAACGGGAAGCGGCGATTATCGGCGGTGGTATTGCCAGCGCGTTGTTGTCGCTGGCGCt < 1:138802/69‑1 (MQ=255)
ggCAGCAACAAACAGGAAGCGGCAATTATTGGAGGCGGTATTGCCAGCGCGTTGTTGTCACTGGCGCt > 1:615609/1‑68 (MQ=255)
ggCAGCAACAAACAGGAAGCGGCAATTATTGGAGGCGGTATTGCCAGCGCGTTGTTGTCACTGGCGCTa > 1:2606371/1‑69 (MQ=255)
ggCAGCAACAAACAGGAAGCGGCAATTATTGGAGGCGGTATTGCCAGCGCGTTGTTGTCACTGGCGCTa > 1:928641/1‑69 (MQ=255)
ggCAGCAACAAACAGGAAGCGGCAATTATTGGAGGCGGTATTGCCAGCGCGTTGTTGTCACTGGCGCTa > 1:450724/1‑69 (MQ=255)
ggCAGCAACAAACAGGAAGCGGCAATTATTGGAGGCGGTATTGCCAGCGCGTTGTTGTCACTGGCGCTa > 1:357443/1‑69 (MQ=255)
ggCAGCAACAAACAGGAAGCGGCAATTATTGGAGGCGGTATTGCCAGCGCGTTGTTGTCACTGGCGCTa > 1:3370903/1‑69 (MQ=255)
ggCAGCAACAAACAGGAAGCGGCAATTATTGGAGGCGGTATTGCCAGCGCGTTGTTGTCACTGGCGCTa > 1:3366634/1‑69 (MQ=255)
ggCAGCAACAAACAGGAAGCGGCAATTATTGGAGGCGGTATTGCCAGCGCGTTGTTGTCACTGGCGCTa > 1:3012588/1‑69 (MQ=255)
ggCAGCAACAAACAGGAAGCGGCAATTATTGGAGGCGGTATTGCCAGCGCGTTGTTGTCACTGGCGCTa > 1:2620802/1‑69 (MQ=255)
ggCAGCAACAAACAGGAAGCGGCAATTATTGGAGGCGGTATTGCCAGCGCGTTGTTGTCACTGGCGCTa > 1:254795/1‑69 (MQ=255)
ggCAGCAACAAACAGGAAGCGGCAATTATTGGAGGCGGTATTGCCAGCGCGTTGTTGTCACTGGCGCTa > 1:2503185/1‑69 (MQ=255)
ggCAGCAACAAACAGGAAGCGGCAATTATTGGAGGCGGTATTGCCAGCGCGTTGTTGTCACTGGCGCTa > 1:2457787/1‑69 (MQ=255)
ggCAGCAACAAACAGGAAGCGGCAATTATTGGAGGCGGTATTGCCAGCGCGTTGTTGTCACTGGCGCTa > 1:2169908/1‑69 (MQ=255)
ggCAGCAACAAACAGGAAGCGGCAATTATTGGAGGCGGTATTGCCAGCGCGTTGTTGTCACTGGCGCTa > 1:1253366/1‑69 (MQ=255)
ggCAGCAACAAACAGGAAGCGGCAATTATTGGAGGCGGTATTGCCAGCGCGTTGTTGTCACTGGCGCTa > 1:1585926/1‑69 (MQ=255)
ggCAGCAACAAACAGGAAGCGGCAATTATTGGAGGCGGTATTGCCAGCGCGTTGTTGTCACTGGCGCTa > 1:1868333/1‑69 (MQ=255)
gcagcagcaAACGGGAAGCGGCGATTATCGGCGGTGGTATTGCCAGCGCGTTGTTGTCGCTGGCGCTAt < 1:57909/69‑1 (MQ=255)
aaaCGGGAAGCGGCGATTATCGGCGGTGGTATTGCCAGCGCGTTGTTGTCGCTGGCGCTATTACGgcgc < 1:3078851/69‑1 (MQ=255)
aaaCGGGAAGCGGCGATTATCGGCGGTGGTATTGCCAGCGCGTTGTTGTCGCTGGCGCTATTACGgcgc < 1:547191/69‑1 (MQ=255)
aaaCGGGAAGCGGCGATTATCGGCGGTGGTATTGCCAGCGCGTTGTTGTCGCTGGCGCTATTACGgcgc < 1:546325/69‑1 (MQ=255)
aaaCGGGAAGCGGCGATTATCGGCGGTGGTATTGCCAGCGCGTTGTTGTCGCTGGCGCTATTACGgcgc < 1:2029145/69‑1 (MQ=255)
gCCAGCGCGTTGTTGTCGCTGGCGCTATTACGGCGCGGCTGGCAGGTAACGCTTTATTGCGCGGATGAg < 1:2085384/69‑1 (MQ=255)
gCCAGCGCGTTGTTGTCGCTGGCGCTATTACGGCGCGGCTGGCAGGTAACGCTTTATTGCGCGGATGAg < 1:902956/69‑1 (MQ=255)
gCCAGCGCGTTGTTGTCGCTGGCGCTATTACGGCGCGGCTGGCAGGTAACGCTTTATTGCGCGGATGAg < 1:2788132/69‑1 (MQ=255)
gCCAGCGCGTTGTTGTCGCTGGCGCTATTACGGCGCGGCTGGCAGGTAACGCTTTATTGCGCGGATGAg < 1:2797754/69‑1 (MQ=255)
aGCGCGTTGTTGTCACTGGCGCTATTGCGTCGCGGCTGGCAg > 1:1304317/1‑42 (MQ=37)
aGCGCGTTGTTGTCACTGGCGCTATTGCGTCGCGGCTGGCAGGTAACGCTTTGTTGCGCgg > 1:3136566/1‑61 (MQ=255)
aGCGCGTTGTTGTCACTGGCGCTATTGCGTCGCGGCTGGCAGGTAACGCTTTAt > 1:1907035/1‑54 (MQ=38)
aGCGCGTTGTTGTCACTGGCGCTATTGCGTCGCGGCTGGCAGGTAACGCTTTATTGCGCgg > 1:1215840/1‑61 (MQ=255)
aGCGCGTTGTTGTCACTGGCGCTATTGCGTCGCGGCTGGCAGGTAACGCTTTATTGCGCgg > 1:1300823/1‑61 (MQ=255)
aGCGCGTTGTTGTCACTGGCGCTATTGCGTCGCGGCTGGCAGGTAACGCTTTATTGCGCgg > 1:2469039/1‑61 (MQ=255)
aGCGCGTTGTTGTCACTGGCGCTATTGCGTCGCGGCTGGCAGGTAACGCTTTATTGCGCgg > 1:1343247/1‑61 (MQ=255)
aGCGCGTTGTTGTCACTGGCGCTATTGCGTCGCGGCTGGCAGGTAACGCTTTATTGCGCgg > 1:1490643/1‑61 (MQ=255)
aGCGCGTTGTTGTCACTGGCGCTATTGCGTCGCGGCTGGCAGGTAACGCTTTATTGCGCgg > 1:3279625/1‑61 (MQ=255)
aGCGCGTTGTTGTCACTGGCGCTATTGCGTCGCGGCTGGCAGGTAACGCTTTATTGCGCgg > 1:3144857/1‑61 (MQ=255)
aGCGCGTTGTTGTCACTGGCGCTATTGCGTCGCGGCTGGCAGGTAACGCTTTATTGCGCgg > 1:3098534/1‑61 (MQ=255)
aGCGCGTTGTTGTCACTGGCGCTATTGCGTCGCGGCTGGCAGGTAACGCTTTATTGCGCgg > 1:2124634/1‑61 (MQ=255)
aGCGCGTTGTTGTCACTGGCGCTATTGCGTCGCGGCTGGCAGGTAACGCTTTATTGCGCgg > 1:307018/1‑61 (MQ=255)
aGCGCGTTGTTGTCACTGGCGCTATTGCGTCGCGGCTGGCAGGTAACGCTTTATTGCGCgg > 1:1594879/1‑61 (MQ=255)
aGCGCGTTGTTGTCACTGGCGCTATTGCGTCGCGGCTGGCAGGTAACGCTTTATTGCGCgg > 1:3009267/1‑61 (MQ=255)
aGCGCGTTGTTGTCACTGGCGCTATTGCGTCGCGGCTGGCAGGTAACGCTTTATTGCGCgg > 1:1708951/1‑61 (MQ=255)
aGCGCGTTGTTGTCACTGGCGCTATTGCGTCGCGGCTGGCAGGTAACGCTTTATTGCGCgg > 1:2602510/1‑61 (MQ=255)
aGCGCGTTGTTGTCACTGGAGCTATTGCGTCGCGGCTGGCAGGTAACGCTTTATTGCGCgg > 1:2439845/1‑61 (MQ=38)
gttgtCGCTGGCGCTATTACGGCGCGGCTGGCAGGTAACGCTTTATTGCGCGGATGAGGCCCCCGCACt > 1:3278879/1‑69 (MQ=255)
|
CACGGGCAGCAGCAAACGGGAAGCGGCGATTATCGGCGGTGGTATTGCCAGCGCGTTGTTGTCGCTGGCGCTATTACGGCGCGGCTGGCAGGTAACGCTTTATTGCGCGGATGAGGCCCCCGCACT > minE/1527792‑1527917
|
| 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
