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 F36 I1 R1
|
19 |
36.4 |
1272818 |
94.0% |
1196448 |
142.2 |
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%
| 60.6
/ 15.8
| 25 | coding (40/1389 nt) | narU | nitrate/nitrite transporter |
| Reads supporting (aligned to +/- strand): ref base . (4/2); new base A (13/6); total (17/8) |
| 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 |
| * | NC_000913_3_pae_tpiA | 1,544,022 | 0 | C | A | 92.0%
| 67.6
/ ‑4.8
| 25 | L13F (TTG→TTT) | narU | nitrate/nitrite transporter |
| Reads supporting (aligned to +/- strand): ref base C (2/0); new base A (15/8); total (17/8) |
| 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 |
TTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑C‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAA > NC_000913_3_pae_tpiA/1543885‑1544170
|||
ttAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGATGGCCGGATTTTCTGGTTTCCAGTCGCG‑CAA‑AAAGATAAc > 1:593971/1‑149 (MQ=255)
ggTAACTGCGCTAAATAGCATCCAGACCCGAAAGCCAAGATGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGCCGCGAA‑A‑AAAGATAACGACTa > 2:298579/1‑149 (MQ=255)
aGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCa < 2:162503/149‑1 (MQ=255)
tCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑AAA‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGc > 2:107460/1‑149 (MQ=255)
cAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCAAGAGATTTCTTCGCGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑A‑ATAAAGATAACGACTCTTTTTTTCATTTTGCAGTGcaa > 2:250583/1‑147 (MQ=255)
gCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTca < 1:414804/149‑1 (MQ=255)
aagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGc > 1:268009/1‑149 (MQ=255)
tgactgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTa > 1:451317/1‑149 (MQ=255)
ccAGAGAGTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaaaaaa < 1:6517/149‑1 (MQ=255)
cAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCCCTTGCACACATTGGTAATaaaaaaaat > 1:553194/1‑148 (MQ=255)
agagATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑CAA‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACCCATTCGTTATGGAAAAAAgc > 2:259910/1‑148 (MQ=255)
tttCTTGAATCAATATGCTTTCCTTTAATTTCTCAGAAAGCCGGATTTTCTGTTTTCCAGTCGCG‑AAA‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACaaaa < 2:194198/149‑1 (MQ=255)
tttCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACaaaa > 1:595898/1‑149 (MQ=255)
ttcttcGAGCAATATGTTTTCCTTTATTTTCCCAGCAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAACGACAAAac > 2:48571/1‑149 (MQ=255)
tcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGa < 1:107460/149‑1 (MQ=255)
aGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGt > 1:389173/1‑149 (MQ=255)
gTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTACCAGTCGCGAA‑A‑AAAGATAACAACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCACACATGCACACATTGGTAATGAAAAAAAGCCAGAACAGGAGGTAAAgcgaa > 1:362832/1‑147 (MQ=255)
tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCa > 1:555957/1‑149 (MQ=255)
tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCACTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAGAAACAATACACACAGTCACGCCCAATAGccc > 2:165305/1‑148 (MQ=255)
atgaTTTGCCCAGAAGGGCAGGTTTTCTGGTTGCCAGGCCCGAA‑A‑AAAGATAACGACTATTTTTCACATTTTGCAGTGCCATATTGTCCCTCACCTGCACACATTGGTAATGAAAAAAAGACAAAACACGTGGTAAGGCGCAATAGCCa < 2:28276/146‑1 (MQ=255)
aTTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCt > 2:229074/1‑88 (MQ=255)
aTTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCt < 1:229074/88‑1 (MQ=255)
ccGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAAAAAACGACTATTTTTCTCATTTTGCAGTGCCAAATTTTTCCCCCCATGCACACATTGGTAATGAAAAAAAGACAAAAAAACAGGTAAGGCGCAAAAACCAGTTAATAGAAATAAGGa > 2:20242/1‑149 (MQ=255)
gTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTCAGGCGCAATAGCCAGTTATTAGAATGAAAGATGAATTggtgca > 2:116768/1‑145 (MQ=255)
tttCCAGTCGCG‑AAA‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGaa < 1:20242/149‑1 (MQ=255)
aa‑aaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGaaa < 1:224800/148‑1 (MQ=255)
|||
TTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑C‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAA > NC_000913_3_pae_tpiA/1543885‑1544170
|
| 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
