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 |
|
A21 F73 I1 R1
|
19 |
39.3 |
1399748 |
93.9% |
1314363 |
140.8 |
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 | 76.0%
| 60.3
/ 18.4
| 25 | coding (40/1389 nt) | narU | nitrate/nitrite transporter |
| Reads supporting (aligned to +/- strand): ref base . (3/3); new base A (9/10); total (12/13) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.03e-01 |
| * | NC_000913_3_pae_tpiA | 1,544,022 | 0 | C | A | 100.0%
| 77.5
/ NA
| 25 | L13F (TTG→TTT) | narU | nitrate/nitrite transporter |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (12/13); total (12/13) |
TATTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑C‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAA > NC_000913_3_pae_tpiA/1543877‑1544170
|||
tATTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑a‑aaa > 1:397674/1‑149 (MQ=255)
ttGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑A‑aaaaa < 1:545780/149‑2 (MQ=255)
ttGAGATTAACGGTAACTGCGCGAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑A‑aaaaa < 2:37904/149‑2 (MQ=255)
tAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGCTTTTCTGGTTTACAGTCGCGAA‑AAAAGATAACTAATATTTTATTCAtt > 2:329766/1‑149 (MQ=255)
aTCCAGACACAGAAGGAAAAAAGTAGACAACTGACTGATATCCAGAGATTTCTTCTAGCAATAGGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTg > 2:588457/1‑149 (MQ=255)
tCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑AAAAAAGATAACGACTATTTTTCTCATTTTGCAGTGc > 1:290577/1‑149 (MQ=255)
acaaGACACAGAAGGCATGAAGCACACGACTGACTGATATCCAGACATTTCTTCGATCAATATGTTTTCCGTGATTTTCCCAGAAGGCCGGATTTTCTGGTTACCAATCGAGAA‑AAAAGATAACGACTACTTTTCTCATTCTGCAGTGc < 2:590906/146‑1 (MQ=255)
cAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑A‑aaaaagata > 2:434720/1‑115 (MQ=255)
cAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑A‑aaaaagata < 1:434720/120‑6 (MQ=255)
acaGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCACTGCCATATTg > 1:262653/1‑149 (MQ=255)
gAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTc < 2:397674/149‑1 (MQ=255)
aaGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATACCGACTATTTTTCTCATTTTGCAGTGCCATATTGTTcc > 1:191938/1‑149 (MQ=255)
cAACTTACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGTATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACAtt < 2:552343/149‑1 (MQ=255)
actgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACGAGTTGTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAAt < 1:312985/149‑1 (MQ=255)
agagATTTCTTCGCGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGTCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGa < 2:414278/149‑1 (MQ=255)
agagATTCCTCCGAGTAACTCGTTTTCTGTTATTTGCACAGAAGGCCGTATTTTCTGTTTTCCAGTAGCGAA‑AAAAGATATCGACTATTTTTCGCATTTTGCAGTGCCATATTGTTCCTCACATGCACATATTGGTAATGAAAAAAAGa < 2:65892/149‑1 (MQ=255)
tatGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑AAAAAAGATAACGACTATTTTTCTCATTTTGCAGTACCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGgc > 2:695880/1‑149 (MQ=255)
tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCa > 1:649067/1‑149 (MQ=255)
ttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGACATATTGTTCCTCACATGCACACGTTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCAAg > 2:197175/1‑149 (MQ=255)
ttATTCTCCCAGAAGGTCCGATTTTCTTGTTTCCAGTAACAAA‑AAAAGATAACGACTATGTTGCTCATTTTGCAGTGCCAGATTGTTCCTCACATGCACACATTGGTACTTAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAg < 2:359209/149‑1 (MQ=255)
aTTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGtt < 1:588457/149‑1 (MQ=255)
tCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGttatta > 2:619602/1‑149 (MQ=255)
tCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGttatta > 1:489345/1‑149 (MQ=255)
cAGAAGGCCGGATTATCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGac > 1:604045/1‑148 (MQ=255)
aGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTaa < 1:164507/149‑1 (MQ=255)
aTTTTCTGGTTTCCAGTCTCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGaa < 2:174845/149‑1 (MQ=255)
cgcgaaaaaaTATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGAt < 1:695817/143‑1 (MQ=255)
gcgaaaaaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGAtt < 2:290577/144‑1 (MQ=255)
aaaaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTc < 2:126915/48‑1 (MQ=255)
aaaaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTc > 1:126915/2‑49 (MQ=255)
aaaaaGATAAAGACTATTTTTCTCATGTTTCAGTGCCATATTTTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGaaa < 2:478333/148‑1 (MQ=255)
|||
TATTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑C‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAA > NC_000913_3_pae_tpiA/1543877‑1544170
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
