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 |
|
A17 F133 I1 R1
|
18 |
54.6 |
2042212 |
95.3% |
1946228 |
140.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913_3_pae_tpiA |
1,544,022 |
1 bp→AA |
coding (39/1389 nt) |
narU ← |
nitrate/nitrite transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913_3_pae_tpiA | 1,544,021 | 1 | . | A | 92.9%
| 139.2
/ 4.8
| 42 | coding (40/1389 nt) | narU | nitrate/nitrite transporter |
| Reads supporting (aligned to +/- strand): ref base . (3/0); new base A (18/21); total (21/21) |
| Fisher's exact test for biased strand distribution p-value = 2.32e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| * | NC_000913_3_pae_tpiA | 1,544,022 | 0 | C | A | 100.0%
| 147.5
/ NA
| 42 | L13F (TTG→TTT) | narU | nitrate/nitrite transporter |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (21/21); total (21/21) |
AACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑C‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAA > NC_000913_3_pae_tpiA/1543887‑1544170
|||
aaCGGTAACTACGCGAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGCCTGATATCCAGAGATGTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGAc > 4:223766/1‑150 (MQ=255)
gcgcTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑AAA‑AAAGATAACGACTATTTTtctc > 1:509868/1‑150 (MQ=255)
gcgcTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTAAAGAAGAGAA‑A‑AAAGATAACGACTATTTTtctc < 2:587233/150‑1 (MQ=255)
cAGACACAGAATGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTACCAGAAGGCCGGATTTTCTGGTTAAAAAAAAAAAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCat < 4:210005/150‑1 (MQ=255)
aGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTc < 1:579599/150‑1 (MQ=255)
aGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTATTc > 3:97584/1‑150 (MQ=255)
aaGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCt > 1:480102/1‑150 (MQ=255)
aGGCAAGAAGTAGACAACTGACTGATATCCAGAAATTGCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATGGTTCGCATTTTGCAGTGCCATATTGTTCCTc < 3:182592/150‑1 (MQ=255)
cAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCCTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTcaca > 1:366719/1‑150 (MQ=255)
gaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTGTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGc < 2:329164/150‑1 (MQ=255)
tAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACTACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGcacac > 4:59592/1‑150 (MQ=255)
ctgactgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTa < 1:280624/150‑1 (MQ=255)
ctgactgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTa < 4:206935/150‑1 (MQ=255)
gaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaa < 2:392425/150‑1 (MQ=255)
ccAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTAt > 4:81115/1‑90 (MQ=255)
ccAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTAt < 3:81115/90‑1 (MQ=255)
cAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGa > 2:349272/1‑150 (MQ=255)
cAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGa > 3:212896/1‑150 (MQ=255)
cAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGa > 3:161778/1‑150 (MQ=255)
cAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGa < 1:604306/150‑1 (MQ=255)
cAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGACGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGa < 4:131914/150‑1 (MQ=255)
cAGAGATTTCCTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGa > 3:161765/1‑150 (MQ=255)
aTTTCTTTGAGCAATATGTTTTCCTTTATTTTCCAAGAAGGACTGATTTACAGTTCACCAGTCGAGAA‑A‑AAACATACCGACAATTAATCTCAACTTGCAGTGCCATATTGTTCCTCACCTACACAAAAAAAAAAAAAAAAAAAGACaaaa < 4:148173/150‑1 (MQ=255)
aTTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACTACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACaaaa < 3:59592/150‑1 (MQ=255)
aTTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGACGAATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACAATAAAAATAAAAAAAAGACaaaa < 2:497593/150‑1 (MQ=255)
cttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTg < 1:431699/93‑1 (MQ=255)
cttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑AAA‑AAAGATAACGACTATTTTTCTCATTTTg > 2:431699/1‑93 (MQ=255)
cGAGCAATATGTTCTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAgg < 4:326580/150‑1 (MQ=255)
atatGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCata < 4:338730/94‑1 (MQ=255)
atatGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCata > 3:338730/1‑94 (MQ=255)
ttttCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATCAAAAAAAGACAAAACACGAGGTAAGGCGCAAt > 4:212131/1‑150 (MQ=255)
cTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCa < 1:115314/150‑1 (MQ=255)
cTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCa > 3:41682/1‑150 (MQ=255)
tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAg > 1:37303/1‑150 (MQ=255)
tATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑A‑ACACAGATAACGACTATTTTTCTCAATTTGCAGTACCATATTGTTCCTCACATGCACCCATTGGTAATGAAACAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGtt > 2:285109/1‑150 (MQ=255)
ttttCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGttat < 3:329084/150‑1 (MQ=255)
tttCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGttatt > 4:102639/1‑150 (MQ=255)
aaGGCCGGATTTTCTGGTTTACAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACAAAAAAAAAAAAAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTaa < 4:246726/150‑1 (MQ=255)
cGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTg < 3:202451/55‑1 (MQ=255)
cGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTg > 4:202451/1‑55 (MQ=255)
tCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTggg > 1:339348/1‑150 (MQ=255)
tttCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAg > 2:445800/1‑150 (MQ=255)
tcgcgaaa‑aaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGAt < 3:187360/143‑1 (MQ=255)
gcgaaa‑aaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTg > 3:146227/6‑150 (MQ=255)
gcgaaa‑aaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTg < 4:97584/145‑1 (MQ=255)
aaa‑aaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGaaa < 1:397006/148‑1 (MQ=255)
aaa‑aaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGaaa > 2:398876/3‑150 (MQ=255)
|||
AACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑C‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAA > NC_000913_3_pae_tpiA/1543887‑1544170
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
