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 |
2,662,258 |
G→A |
100% |
P191S (CCC→TCC) |
rtcR ← |
sigma 54‑dependent transcriptional regulator of rtcBA expression |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,662,258 | 0 | G | A | 79.1%
| 21.0
/ 1.1
| 19 | P191S (CCC→TCC) | rtcR | sigma 54‑dependent transcriptional regulator of rtcBA expression |
| Reads supporting (aligned to +/- strand): ref base G (2/2); new base A (15/0); total (17/2) |
| Fisher's exact test for biased strand distribution p-value = 3.51e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
AATCGGCGCGCGGGATTTGATCGCCACTTTTTCGATCTGCTCAATCATGCGGTTGAAGTGGGGGTTACGCGTGGCAATGCCGGACTTAAGAAAATCAAGCGTTTGCTGGCGTTCCTCGGCAAAGCGGCTG > minE/2662196‑2662325
|
gaTCGGTGCGCGGGATTTGATCGCCACTTTTTCGATCTGCTCAATCATGCGGTTGAAGTGGGAGTTAcg > 1:2662199/2‑69 (MQ=255)
gaTCGGTGCGCGGGATTTGATCGCCACTTTTTCGATCTGCTCAATCATGCGGTTGAAGTGGGAGTTAcg > 1:934515/2‑69 (MQ=255)
gaTCGGTGCGCGGGATTTGATCGCCACTTTTTCGATCTGCTCAATCATGCGGTTGAAGTGGGAGTTAcg > 1:667320/2‑69 (MQ=255)
gaTCGGTGCGCGGGATTTGATCGCCACTTTTTCGATCTGCTCAATCATGCGGTTGAAGTGGGAGTTAcg > 1:532590/2‑69 (MQ=255)
gaTCGGTGCGCGGGATTTGATCGCCACTTTTTCGATCTGCTCAATCATGCGGTTGAAGTGGGAGTTAcg > 1:479576/2‑69 (MQ=255)
gaTCGGTGCGCGGGATTTGATCGCCACTTTTTCGATCTGCTCAATCATGCGGTTGAAGTGGGAGTTAcg > 1:343141/2‑69 (MQ=255)
gaTCGGTGCGCGGGATTTGATCGCCACTTTTTCGATCTGCTCAATCATGCGGTTGAAGTGGGAGTTAcg > 1:3415013/2‑69 (MQ=255)
gaTCGGTGCGCGGGATTTGATCGCCACTTTTTCGATCTGCTCAATCATGCGGTTGAAGTGGGAGTTAcg > 1:3307145/2‑69 (MQ=255)
gaTCGGTGCGCGGGATTTGATCGCCACTTTTTCGATCTGCTCAATCATGCGGTTGAAGTGGGAGTTAcg > 1:3038409/2‑69 (MQ=255)
gaTCGGTGCGCGGGATTTGATCGCCACTTTTTCGATCTGCTCAATCATGCGGTTGAAGTGGGAGTTAcg > 1:3009765/2‑69 (MQ=255)
gaTCGGTGCGCGGGATTTGATCGCCACTTTTTCGATCTGCTCAATCATGCGGTTGAAGTGGGAGTTAcg > 1:1014204/2‑69 (MQ=255)
gaTCGGTGCGCGGGATTTGATCGCCACTTTTTCGATCTGCTCAATCATGCGGTTGAAGTGGGAGTTAcg > 1:2651374/2‑69 (MQ=255)
gaTCGGTGCGCGGGATTTGATCGCCACTTTTTCGATCTGCTCAATCATGCGGTTGAAGTGGGAGTTAcg > 1:2315246/2‑69 (MQ=255)
gaTCGGTGCGCGGGATTTGATCGCCACTTTTTCGATCTGCTCAATCATGCGGTTGAAGTGGGAGTTAcg > 1:1595488/2‑69 (MQ=255)
gaTCGGTGCGCGGGATTTGATCGCCACTTTTTAGATCTGCTCAATCATGCGGTTGAAGTGGGAGTTAcg > 1:2494273/2‑69 (MQ=255)
tCGGCGCGCGGGATTTGATCGCCACTTTTTCGATCTGCTCAATCATGCGGTTGAAGTGGGGGTTAcgcg < 1:2604080/69‑1 (MQ=255)
tCGGCGCGCGGGATTTGATCGCCACTTTTTCGATCTGCTCAATCATGCGGTTGAAGTGGGGGTTAcgcg < 1:3231954/69‑1 (MQ=255)
cGGTTGAAGTGGGGGTTACGCGTGGCAATGCCGGACTTAAGAAAATCAAGCGTTTGCTGGCGTTCCTc > 1:861620/1‑68 (MQ=255)
cGGTTGAAGTGGGGGTTACGCGTGGCAATGCCGGACTTAAGAAAATCAAGCGTTTGCTGGCGTTCCTc > 1:3112263/1‑68 (MQ=255)
gggggTTACGCGTGGCAATGCCGGACTTAAGAAAATCAAGCGTTTGCTGGCGTTCCTCGGCAAAGCGGc > 1:624735/1‑69 (MQ=255)
gggggTTACGCGTGGCAATGCCGGACTTAAGAAAATCAAGCGTTTGCTGGCGTTCCTCGGCAAAGCGGc > 1:1268875/1‑69 (MQ=255)
gggggTTACGCGTGGCAATGCCGGACTTAAGAAAATCAAGCGTTTGCTGGCGTTCCTCGGCAAAGCGGc > 1:1559472/1‑69 (MQ=255)
gggagTTACGCGTGGCAATGCCGGACTTAAGAAAATCAAGCGTTTGCTGGCGTTCCTCGGCAAAGCgg > 1:1167339/1‑68 (MQ=255)
gggagTTACGCGTGGCAATGCCGGACTTAAGAAAATCAAGCGTTTGCTGGCGTTCCTCGGCAAAGCGGc > 1:1138739/1‑69 (MQ=255)
gggagTTACGCGTGGCAATGCCGGACTTAAGAAAATCAAGCGTTTGCTGGCGTTCCTCGGCAAAGCGGc > 1:2392569/1‑69 (MQ=255)
gggagTTACGCGTGGCAATGCCGGACTTAAGAAAATCAAGCGTTTGCTGGCGTTCCTCGGCAAAGCGGc > 1:737210/1‑69 (MQ=255)
gggagTTACGCGTGGCAATGCCGGACTTAAGAAAATCAAGCGTTTGCTGGCGTTCCTCGGCAAAGCGGc > 1:648790/1‑69 (MQ=255)
gggagTTACGCGTGGCAATGCCGGACTTAAGAAAATCAAGCGTTTGCTGGCGTTCCTCGGCAAAGCGGc > 1:1556225/1‑69 (MQ=255)
gggagTTACGCGTGGCAATGCCGGACTTAAGAAAATCAAGCGTTTGCTGGCGTTCCTCGGCAAAGCGGc > 1:2112883/1‑69 (MQ=255)
gggagTTACGCGTGGCAATGCCGGACTTAAGAAAATCAAGCGTTTGCTGGCGTTCCTCGGCAAAGCGGc > 1:3018467/1‑69 (MQ=255)
gggagTTACGCGTGGCAATGCCGGACTTAAGAAAATCAAGCGTTTGCTGGCGTTCCTCGGCAAAGCGGc > 1:2135135/1‑69 (MQ=255)
gggagTTACGCGTGGCAATGCCGGACTTAAGAAAATCAAGCGTTTGCTGGCGTTCCTCGGCAAAGCGGc > 1:2955111/1‑69 (MQ=255)
gggagTTACGCGTGGCAATGCCGGACTTAAGAAAATCAAGCGTTTGCTGGCGTTCCTCGGCAAAGCGGc > 1:2231720/1‑69 (MQ=255)
gggagTTACGCGTGGCAATGCCGGACTTAAGAAAATCAAGCGTTTGCTGGCGTTCCTCGGCAAAGCGGc > 1:2439758/1‑69 (MQ=255)
gggagTTACGCGTGGCAATGCCGGACTTAAGAAAATCAAGCGTTTGCTGGCGTTCCTCGGCAAAGCGGc > 1:2403169/1‑69 (MQ=255)
gggagTAACGCGTGGCAATGCCGGACTTAAGAAAATCAAGCGTTTGCTGGCGTTCCTCGGCAAAGCGGc > 1:439523/1‑69 (MQ=255)
gggTTACGCGTGGCAATGCCGGACTTAAGAAAATCAAGCGTTTGCTGGCGTTCCTCGGCAAAGCGGCTg > 1:1715532/1‑69 (MQ=255)
|
AATCGGCGCGCGGGATTTGATCGCCACTTTTTCGATCTGCTCAATCATGCGGTTGAAGTGGGGGTTACGCGTGGCAATGCCGGACTTAAGAAAATCAAGCGTTTGCTGGCGTTCCTCGGCAAAGCGGCTG > minE/2662196‑2662325
|
| 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
