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 |
|
A1 F28 I1 R1
|
163 |
52.9 |
1786516 |
99.3% |
1774010 |
139.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,563,254 |
C→T |
intergenic (+137/‑338) |
yffP → / → yffQ |
CPZ‑55 prophage; uncharacterized protein YffP/CPZ‑55 prophage; uncharacterized protein YffQ |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,563,254 | 0 | C | T | 92.0%
| 70.3
/ ‑1.4
| 25 | intergenic (+137/‑338) | yffP/yffQ | CPZ‑55 prophage; uncharacterized protein YffP/CPZ‑55 prophage; uncharacterized protein YffQ |
| Reads supporting (aligned to +/- strand): ref base C (1/1); new base T (2/21); total (3/22) |
| Fisher's exact test for biased strand distribution p-value = 2.30e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AATTTTCGGACAAACGCGCGCGTAGCCGACGTCAGCGGCAAGACTGGCGGTCATTTCCCCGCTCCTACGCGAAAAATCCCTCACAACTACCCTGCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCACAATTGATTAATTTCTGA > NC_000913/2563117‑2563375
|
aaTTTTCGGACAAACGCGCGCGTAGCCGACGTCAGCGGCAAGACTGGCGGTCATTTCCCCGCTCCTACGCGAAAAATCCCTCACAACTACCCTGCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCTAg > 1:309890/1‑140 (MQ=255)
aTTTTCGGACAAACGCGCGCGTAGCCGACGTCAGCGGCAAGACTGGCGGTCATTTCCCCGCTCCTACGCGAAAAATCCCTCACAACTACCCTGCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCTAgg < 1:77674/140‑1 (MQ=255)
ttttCGGACAAACGCGCGCGTAGCCGACGTCAGCGGCAAGACTGGCGGTCATTTCCCCGCTCCTACGCGAAAAATCCCTCACAACTACCCTGCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCTAGGc < 2:223822/140‑1 (MQ=255)
ttttCGGACAAACGCGCGCGTAGCCGACGTCAGCGGCAAGACTGGCGGTCATTTCCCCGCTCCTACGCGAAAAATCCCTCACAACTACCCTGCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCTAGGc < 2:118072/140‑1 (MQ=255)
ttttCGGACAAACGCGCGCGTAGCCGACGTCAGCGGCAAGACTGGCGGTCATTTCCCCGCCCCTACGCGAAAAATCCCTCACAACTACCCTGCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCTAGGc > 2:683634/1‑140 (MQ=255)
cGGACAAACGCGCGCGTAGCCGACGTCAGCGGCAAGACTGGCGGTCATTTCCCCGCTCCTACGCGAAAAATCCCTCACAACTACCCTGCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCTAGGCAGtt < 1:502987/140‑1 (MQ=255)
aaCGCGCGCGTAGCCGACGTCAGCGGCAAGACTGGCGGTCATTTCCCCGCTCCTACGCGAAAAATCCCTCACAACTACCCTGCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCTAGGCAGTTAGCAAc < 2:600899/140‑1 (MQ=255)
gCCGACGTCAGCGGCAAGACTGGCGGTCATTTCCCCGCTCCTACGCGAAAAATCCCTCACAACTACCCTGCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCTAGGCAGTTAGCAACCTACCCGGGCCt < 1:798509/140‑1 (MQ=255)
gCCGACGTCAGCGGCAAGACTGGCGGTCATTTCCCCGCTCCTACGCGAAAAATCCCTCACAACTACCCTGCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCTAGGCAGTTAGCAACCTACCCGGGCCt < 1:69132/140‑1 (MQ=255)
cGACGTCAGCGGCAAGACTGGCGGTCATTTCCCCGCTCCTACGCGAAAAATCCCTCACAACTACCCTGCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCTAGGCAGTTAGCAACCTACCCGGGCCttt < 2:727676/140‑1 (MQ=255)
cGTCAGCGGCAAGACTGGCGGTCATTTCCCCGCTCCTACGCGAAAAATCCCTCACAACTACCCTGCAAATTTTCCAGATTTTACGTACACGCGCCAAAAATAAA‑GCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTca > 1:746702/1‑140 (MQ=255)
gTCAGCGGCAAGACTGGCGGTCATTTCCCCGCTCCTACGCGAAAAATCCCTCACAACTACCCTGCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCTAGGCAGTTAGCAACCTACCCGGGCCTTTCTca < 2:729119/140‑1 (MQ=255)
aGCGGCAAGACTGGCGGTCATTTCCCCGCTCCTACGCGAAAAATCCCTCACAACTACCCTGCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCTAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACaa < 1:228135/140‑1 (MQ=255)
cAAGACTGGCGGTCATTTCCCCGCTCCTACGCGAAAAATCCCTCACAACTACCCTGCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAAGCCCAGGCAGTTAGGAACTTACCCGGGCCTTTCTCACAATcccc > 2:305321/1‑140 (MQ=255)
gACTGGCGGTCATTTCCCCGCTCCTACGCGAAAAATCCCTCACAACTACCCTGCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCTAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCt < 2:309890/140‑1 (MQ=255)
cTGGCGGTCATTTCCCCGCTCCTACGCGAAAAATCCCTCACAACTACCCTGCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCTAGGCAGTTAGCAACTTACCCGGGCCTTTCTCACAATCCCCGCTGa < 1:305321/140‑1 (MQ=255)
tGGCGGTCATTTCCCCGCTCCTACGCGAAAAATCCCTCACAACTACCCTGCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCTAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGAc < 2:52048/140‑1 (MQ=255)
ggCGGTCATTTCCCCGCTCCTACGCGAAAAATCCCTCACAACTACCCTGCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCTAGGCAGTTAGCAACCTACCAGGGCCTTTCTCACAATCCCCGCTGACa < 1:567974/140‑1 (MQ=255)
ggTCATTTCCCCGCTCCTACGCGAAAAATCCCTCACAACTACCCTGCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCTAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATta < 1:379287/140‑1 (MQ=255)
cTACGCGAAAAATCCCTCACAACTACCCTGCAAATTTACCAGATTTCACGTACACGCGCCAAAAATAAAGGCCTAGGCAGTTAGCAACCTACCCGGGCCCTTCTCACAATCCCTGCTGACATTATATCACCCATATTTcc > 2:789806/1‑140 (MQ=255)
gAAAAATCCCTCACAACTACCCTGCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCTAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTc < 1:361566/140‑1 (MQ=255)
aTCCCTCACAACTACCCTGCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCTAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTg < 1:683634/140‑1 (MQ=255)
gCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCTAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGccgccg < 2:794939/140‑1 (MQ=255)
cAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCTAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGa < 1:849830/140‑1 (MQ=255)
cAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCTAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGa > 2:18112/1‑140 (MQ=255)
aaTTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCTAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACg < 1:789806/140‑1 (MQ=255)
aaTTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCTAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACg < 1:274050/140‑1 (MQ=255)
acGCGCCAAAAATAAA‑GCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCG‑TTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCACAATTGATTAATTTCTGa < 2:746702/140‑1 (MQ=255)
|
AATTTTCGGACAAACGCGCGCGTAGCCGACGTCAGCGGCAAGACTGGCGGTCATTTCCCCGCTCCTACGCGAAAAATCCCTCACAACTACCCTGCAAATTTTCCAGATTTCACGTACACGCGCCAAAAATAAAGGCCCAGGCAGTTAGCAACCTACCCGGGCCTTTCTCACAATCCCCGCTGACATTATATCACCCATCTTTCCGTTTTCAGGTGGGAGACTGATGGCCGCCGACGTTGCACAATTGATTAATTTCTGA > NC_000913/2563117‑2563375
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
