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 |
|
A14 F1 I2 R1
|
774 |
49.2 |
2112398 |
96.9% |
2046913 |
118.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,965,418 |
(GA)4→5 |
coding (213/1266 nt) |
rhlB ← |
ATP‑dependent RNA helicase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,965,410 | 1 | . | G | 95.7%
| 75.2
/ ‑3.2
| 23 | coding (221/1266 nt) | rhlB | ATP‑dependent RNA helicase |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base G (14/8); total (15/8) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01 |
| * | NC_000913 | 3,965,410 | 2 | . | A | 95.7%
| 68.3
/ ‑3.3
| 23 | coding (221/1266 nt) | rhlB | ATP‑dependent RNA helicase |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base A (14/8); total (15/8) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CGTAAGCCAGACCCAGCTTCAGGCCAGTAGCTTCCGCCAGCGGTTCTGCGTCGGCATGGATCTGCACGGCAAGTTCACGCGTCGGTGCCATAATTAAGGCACGCGGCTGATTCACCTTGCGATCGGCAATCGCAGGAT‑‑GAGAGA‑‑GAAGATAATGAAACGTTGACGTAAGAAACGCCATCGTTTTCCCGGTACCGGTTTGCGCCTGCCCGGCTACGTCACGACCCGCCAGCGTCAGCGGAAGGGCCAGTGCCTGAATGGGCG > NC_000913/3965273‑3965533
||
cGTAAGCCAGACCCAGCTTCAGGCCAGTAGCTTCCGCCAGCGGTTCTGCGTCGGCATGGATCTGCACGGCAAGTTCACGCGTCGGTGCCATAATTAAGGCACGCGGCTGATTCACCTTGCGATCGGCAATCGCAGGAT‑‑g < 2:408453/139‑1 (MQ=255)
cAGACCCAGCTTCAGGCCAGTAGCTTCCGCCAGCGGTTCTGCGTCGGCATGGATCTGCACGGCAAGTTCACGCGTCGGTGCCATAATTAAGGCACGCGGCTGATTCACCTTGCGATCGGCAATCGCAGGAT‑‑gagaga‑‑ga < 1:136846/139‑1 (MQ=255)
cAAGTTCACGCGTCGGTGCCATAATTAAGGCACGCGGCTGATTCACCTTGCGATCGGCAATCGCAGGATGAGAGAGA‑‑GAAGATAATGAAACGTTGACGTAAGAAACGCCATCGTTTTCCCGGTACCGGTTTGCGCCTGc > 1:1053896/1‑139 (MQ=255)
cAAGTTCACGCGTCGGTGCCATAATTAAGGCACGCGGCTGATTCACCTTGCGATCGGCAATCGCAGGATGAGAGAGA‑‑GAAGATAATGAAACGTTGACGTAAGAAACGCCATCGTTTTCCCGGTACCGGTTTGCGCCTGc > 1:787758/1‑139 (MQ=255)
cAAGTTCACGCGTCGGTGCCATAATTAAGGCACGCGGCTGATTCACCTTGCGATCGGCAATCGCAGGATGAGAGAGA‑‑GAAGATAATGAAACGTTGACGTAAGAAACGCCATCGTTTTCCCGGTACCGGTTTGCGCCTGc > 2:17697/1‑139 (MQ=255)
cAAGTTCACGCGTCGGTGCCATAATTAAGGCACGCGGCTGATTCACCTTGCGATCGGCAATCGCAGGAT‑‑gagaga‑‑gag > 1:139076/1‑77 (MQ=255)
cAAGTTCACGCGTCGGTGCCATAATTAAGGCACGCGGCTGATTCACCTTGCGATCGGCAATCGCAGGAT‑‑gagaga‑‑gag < 2:139076/78‑2 (MQ=255)
cAAGTTCACGCGTCGGTGCCATAATTAAGGCACGCGGCTGATTCACCTTGCGATCGGCAATCGCAGGAT‑‑gagaga‑‑g < 2:635597/76‑1 (MQ=255)
cAAGTTCACGCGTCGGTGCCATAATTAAGGCACGCGGCTGATTCACCTTGCGATCGGCAATCGCAGGAT‑‑gagaga‑‑g > 1:635597/1‑76 (MQ=255)
cAAGTTCACGCGTCGGTGCCATAATTAAGGCACGCGGCTGATTCACCTTGCGATCGGCAATCGCAGGAT‑‑gag < 1:368362/72‑1 (MQ=255)
cAAGTTCACGCGTCGGTGCCATAATTAAGGCACGCGGCTGATTCACCTTGCGATCGGCAATCGCAGGAT‑‑gag > 2:368362/1‑72 (MQ=255)
cgTCGGTGCCATAATTAAGGCACGCGGCTGATTCACCTTGCGATCGGCAATCGCAGGATGAGAGAGA‑‑GAAGATAATGAAACGTTGACGTAAGAAACGCCATCGTTTTCCCGGTACCGGTTTGCGCCTGCCCGGCTACGt > 2:383739/1‑139 (MQ=255)
gCACGCGGCTGATTCACCTTGCGATCGGCAATCGCAGGATGAGAGAGA‑‑GAAGATAATGAAACGTTGACGTAAGAAACGCCATTGTTTTCCCGGTACCGGTTTGCGCCTGcc < 1:123132/111‑1 (MQ=255)
gCACGCGGCTGATTCACCTTGCGATCGGCAATCGCAGGATGAGAGAGA‑‑GAAGATAATGAAACGTTGACGTAAGAAACGCCATTGTTTTCCCGGTACCGGTTTGCGCCTGcc > 2:123132/1‑111 (MQ=255)
cACGCGGCTGATTCACCTTGCGATCGGCAATCGCAGGATGAGAGAGA‑‑GAAGATAATGAAACGTTGACGTAAGAAACGCCATCGTTTACCCGGTACCGGTTTGCGCCTGCCCGGCTACGTCACGACCCACCAGCGTCCGc < 2:612616/139‑1 (MQ=255)
aCGCGGCTGATTCACCTTGCGATCGGCAATCGCAGGATGAGAGAGA‑‑GAAGATAATGAAACGTTGACGTAAGAAACGCCATCGTTTTCCCGGTACCGGTTTGCGCCTGCCCGGCTACGTCACGACCCGCCAGCGTCAGCg > 2:540084/1‑139 (MQ=255)
cgcgGCTGATTCACCTTGCGATCGGCAATCGCAGGGT‑‑GAGAGAGCGAAGATAATGAAACGTTGACGTAAGAAACGCCATCGTTTTCCCGGTACCGGTTTGCGCCTGCCCCGCTACGTCACGACCCGCCAGCGTCCGCgg > 2:491/1‑139 (MQ=255)
cgcgGCTGATTCACCTTGCGATCGGCAATCGCAGGATGAGAGAGA‑‑GAAGATAATGAAACGTTGACGTAAGAAACGCCATCGTTTTCCCGGTACCGGTTTGCGCCTGCCCGGCTACGTCACGACCCGCCAGCGTCAGCgg > 1:38735/1‑139 (MQ=255)
cgcgGCTGATTCACCTTGCGATCGGCAATCGCAGGATGAGAGAGA‑‑GAAGATAATGAAACGTTGACGTAAGAAACGCCATCGTTTTCCCGGTACCGGTTTGCGCCTGCCCGGCTACGTCACGACCCGCCAGCGTCAGCgg > 2:465292/1‑139 (MQ=255)
gcgGCTGATTCACCTTGCGATCGGCAATCGCAGGATGAGAGAGA‑‑GAAGATAATGAAACGTTGACGTAAGAAACGCCATCGTTTTCCCGGTACCGGTTTGCGCCTGCCCGGCTACGTCACGACCCGCCAGCGTCAGCGGa < 1:465292/139‑1 (MQ=255)
cgGCTGATTCACCTTGCGATCGGCAATCGCAGGATGAGAGAGA‑‑GAAGATAATGAAACGTTGACGTAAGAAACGCCATCGTTTTCCCGGTACCGGTTTGCGCCTGCCCGGCTACGTCACGACCCGCCAGCGTCAGCGGaa > 2:669796/1‑139 (MQ=255)
cgGCTGATTCACCTTGCGATCGGCAATCGCAGGATGAGAGAGA‑‑GAAGATAATGAAACGTTGACGTAAGAAACGCCATCGTTTTCCCGGTACCGGTTTGCGCCTGCCCGGCTACGTCACGACCCGCCAGCGTCAGCGGaa > 1:585150/1‑139 (MQ=255)
ggCTGATTCACCTTGCGATCGGCAATCGCAGGATGAGAGAGA‑‑GAAGATAATGAAACGTTGACGTAAGAAACGCCATCGTTTTCCCGGTACCGGTTTGCGCCTGCCCGGCTACGTCACGACCCGCCCGCGTCAGCGGTAg > 2:699335/1‑139 (MQ=255)
tGATTCACCTTGCGATCGGCAATCGCAGGATGAGAGAGA‑‑GAAGATAATGAAACGTTGACGTAAGAAACGCCATCGTTTTCCCGGTACCGGTTTGCGCCTGCCCGGCTACGTCACGACCCGCCAGCGTCAGCGGAAGGGc < 2:86064/139‑1 (MQ=255)
tGATTCACCTTGCGATCGGCAATCGCAGGATGAGAGAGA‑‑GAAGATAATGAAACGTTGACGTAAGAAACGCCATCGTTTTCCCGGTACCGGTTTGCGCCTGCCCGGCTACGTCACGACCCGCCAGCGTCAGCGGAAGGGc < 2:1053896/139‑1 (MQ=255)
cGATCGGCAATCGCAGGATGAGAGAGA‑‑GAAGATAATGAAACGTTGACGTAAGAAACGCCATCGTTTTCCCGGTACCGGTTTGCGCCTGCCCGGCTACGTCACGACCCGCCAGCGTCAGCGGAAGGGCCAGTGCCTGAAt > 1:604171/1‑139 (MQ=255)
aTCGGCAATCGCAGGATGAGAGAGA‑‑GAAGATAATGAAACGTTGACGTAAGAAACGCCATCGTTTTCCCGGTACCGGTTTGCGCCTGCCCGGCTACGTCACGACCCGCCAGCGTCAGCGGAAGGGCCAGTGCCTGAATgg > 1:86753/1‑139 (MQ=255)
cGGCAATCGCAGGATGAGAGAGA‑‑GAAGATAATGAAACGTTGACGTAAGAAACGCCATCGTTTTCCCGGTACCGGTTTGCGCCTGCCCGGCTACGTCACGACCCGCCAGCGTCAGCGGAAGGGCCAGTGCCTGAATGGGc > 2:657057/1‑139 (MQ=255)
ggCAATCGCAGGATGAGAGAGA‑‑GAAGATAATGAAACGTTGACGTAAGAAACGCCATCGTTTTCCCGGTACCGGTTTGCGCCTGCCCGGCTACGTCACGACCCGCCAGCGTCAGCGGAAGGGCCAGTGCCTGAATGGGCg < 2:38735/139‑1 (MQ=255)
ggCAATCGCAGGATGAGAGAGA‑‑GAAGATAATGAAACGTTGACGTAAGAAACGCCATCGTTTTCCCGGTACCGGTTTGCGCCTGCCCGGCTACGTCACGACCCGCCAGCGTCAGCGGAAGGGCCAGTGCCTGAATGGGCg < 2:277157/139‑1 (MQ=255)
ggCAATCGCAGGATGAGAGAGA‑‑GAAGATAATGAAACGTTGACGTAAGAAACGCCATCGTTTTCCCGGTACCGGTTTGCGCCTGCCCGGCTACGTCACGACCCGCCAGCGTCAGCGGAAGGGCCAGTGCCTGAATGGGCg < 2:765640/139‑1 (MQ=255)
||
CGTAAGCCAGACCCAGCTTCAGGCCAGTAGCTTCCGCCAGCGGTTCTGCGTCGGCATGGATCTGCACGGCAAGTTCACGCGTCGGTGCCATAATTAAGGCACGCGGCTGATTCACCTTGCGATCGGCAATCGCAGGAT‑‑GAGAGA‑‑GAAGATAATGAAACGTTGACGTAAGAAACGCCATCGTTTTCCCGGTACCGGTTTGCGCCTGCCCGGCTACGTCACGACCCGCCAGCGTCAGCGGAAGGGCCAGTGCCTGAATGGGCG > NC_000913/3965273‑3965533
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
