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 F5 I1 R1
|
17 |
45.4 |
1637102 |
94.6% |
1548698 |
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 | 93.5%
| 103.0
/ 1.0
| 31 | coding (40/1389 nt) | narU | nitrate/nitrite transporter |
| Reads supporting (aligned to +/- strand): ref base . (1/1); new base A (16/13); total (17/14) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.31e-01 |
| * | NC_000913_3_pae_tpiA | 1,544,022 | 0 | C | A | 100.0%
| 104.9
/ NA
| 31 | L13F (TTG→TTT) | narU | nitrate/nitrite transporter |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (17/14); total (17/14) |
TAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑C‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAA > NC_000913_3_pae_tpiA/1543892‑1544169
|||
tAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AA‑AAGATAACGACTAtt > 1:56841/1‑149 (MQ=255)
tGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCCAACGGCCGTATTTTCTGGTTTCCAGTCGCGAA‑AA‑AAGATAACGACTATTTTtc < 1:773237/149‑1 (MQ=255)
tAAACAGCATCCAGACAAAGAAGGCAAGGAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AA‑AAGATAACGACTATTTTTCTCAtt < 2:27336/149‑1 (MQ=255)
aGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCa > 1:523217/1‑149 (MQ=255)
cAGACACAGAAGGCAAGAAGTAGACAACTGACTGCTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCCGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCa < 1:805166/149‑1 (MQ=255)
caGAAGGCAAGAAGTAGACAACCGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGt > 1:495905/1‑149 (MQ=255)
aGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑A‑AACAAGATAACGACTATTTTTCGAATTTTGCAGTGGCATATTGtt > 2:439122/1‑149 (MQ=255)
gAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTTCATTGCCATATTTTTc > 2:693321/1‑149 (MQ=255)
aGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCt < 1:375917/149‑1 (MQ=255)
aagaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTcaca > 1:12232/1‑149 (MQ=255)
gTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTGCTCCCATTcac > 2:160009/1‑149 (MQ=255)
aCAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACAt < 2:390227/149‑1 (MQ=255)
aaCTGACTGATATCCAGAGATTTCTGCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTg < 2:494788/149‑1 (MQ=255)
gactgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCTCGAA‑AA‑AAGATAACGACTATTTTTCTCATATTGCAGTGCCATATCGTTCCCCACATGAACACATTGGTaa < 2:635322/149‑1 (MQ=255)
tgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AA‑AAGATAACGAATATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGa < 1:160009/149‑1 (MQ=255)
agagATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGa > 1:279207/1‑149 (MQ=255)
aTTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACaaa > 2:517846/1‑149 (MQ=255)
tttCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACaaaa > 1:420712/1‑149 (MQ=255)
tttCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACaaaa > 2:787980/1‑149 (MQ=255)
aGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGCAAAAACGACAAAACTCGAggg > 2:121820/1‑148 (MQ=255)
gCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAAAACGAGGTa > 1:532349/1‑149 (MQ=255)
cAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTaa < 2:280213/149‑1 (MQ=255)
cAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑AAAA‑AAGATAACGACTATTTTTCTCATTTTGCAGTTCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTaa < 1:532286/149‑1 (MQ=255)
aaTATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTGCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAg < 2:394917/149‑1 (MQ=255)
ttttCCTTTATTTTCCCAGAAGGCCGGATTTTACGGTTTCCATGCGCGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCaa > 1:809001/1‑149 (MQ=255)
tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAAtggaca > 2:105003/1‑144 (MQ=255)
tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCa < 2:279207/149‑1 (MQ=255)
tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCa > 2:87647/1‑149 (MQ=255)
gcccGGAAGGCCGGATTGTCTGCTTTCCAGTCGCGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCTATATTGTGCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGttatta < 2:227173/148‑1 (MQ=255)
cAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGaa > 1:33729/1‑149 (MQ=255)
cAGTCGCGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGc < 1:735467/149‑1 (MQ=255)
tcaaaaa‑aaGATAACAACGATTGTTCTCATTTTGCAATGCCATATTGTTCGTCACATGCACACATTAGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGAtt < 2:479092/144‑1 (MQ=255)
gaaaa‑aaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGttatta < 1:646964/112‑1 (MQ=255)
gaaaa‑aaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGttatta > 2:646964/4‑115 (MQ=255)
aaaa‑aaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGaa < 1:388066/147‑1 (MQ=255)
|||
TAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑C‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAA > NC_000913_3_pae_tpiA/1543892‑1544169
|
| 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
