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 |
|
A18 F7 I1 R1
|
17 |
36.9 |
1277160 |
95.0% |
1213302 |
141.3 |
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 | 84.2%
| 108.4
/ 15.3
| 38 | coding (40/1389 nt) | narU | nitrate/nitrite transporter |
| Reads supporting (aligned to +/- strand): ref base . (3/3); new base A (17/15); total (20/18) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.61e-01 |
| * | NC_000913_3_pae_tpiA | 1,544,022 | 0 | C | A | 97.4%
| 119.4
/ NA
| 38 | L13F (TTG→TTT) | narU | nitrate/nitrite transporter |
| Reads supporting (aligned to +/- strand): ref base C (0/1); new base A (20/17); total (20/18) |
| Fisher's exact test for biased strand distribution p-value = 4.74e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01 |
ATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CG‑C‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGC > NC_000913_3_pae_tpiA/1543884‑1544161
|||
aTTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATaa > 1:575708/1‑149 (MQ=255)
aggaTCGAGACACAGAAGGAAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCa < 2:482579/146‑1 (MQ=255)
aGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCa > 1:403637/1‑149 (MQ=255)
aTCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTCTTTTTCTCATTTTTCa > 2:299683/1‑146 (MQ=255)
aTCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTAttttt > 2:338268/1‑135 (MQ=255)
aTCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTAttttt < 1:338268/135‑1 (MQ=255)
aTCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCa < 1:299683/146‑1 (MQ=255)
gACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCAGCGTGGCCGGGTTTTCGTGTTTCCAGTCGATT‑A‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCata < 2:137696/149‑1 (MQ=255)
acacAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACAACTATTTTTCTCATTTTGCCGTGCCatat > 2:313588/1‑149 (MQ=255)
aGAAGGCAGGAAGTAGACAACTGGCTGATATCCAGAGATTTCGTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGtt < 2:52956/149‑1 (MQ=255)
gCAAGAAGTAGACAACTGACTGATATCCAGAGATTTGTTAGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTca < 1:498378/149‑1 (MQ=255)
aagaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTcaca > 1:443207/1‑149 (MQ=255)
gTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCATTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGcac < 1:600064/149‑1 (MQ=255)
gACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTGCTCATTTTGCAGTGCCATATTGTTCCACCCAttctcctt > 2:608572/1‑142 (MQ=255)
actgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAAt > 1:367990/1‑149 (MQ=255)
tgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGa > 1:232995/1‑149 (MQ=255)
agagATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CG‑AAAAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGa > 2:241950/1‑149 (MQ=255)
gcgaTTTCTTCGAGCTATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGAc < 1:442855/147‑1 (MQ=255)
tttCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACaaaa > 1:254636/1‑149 (MQ=255)
ttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACg > 1:27028/1‑149 (MQ=255)
ttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CG‑AAAAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATGGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACg > 1:284880/1‑149 (MQ=255)
ttttCCTTTATTTGCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAC‑AAAAGCTCACTGCTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCaa < 1:313588/149‑1 (MQ=255)
tttCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAAt > 2:210292/1‑149 (MQ=255)
tCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CG‑AAAAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCCCATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAg > 2:316298/1‑149 (MQ=255)
ccTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGc < 2:575708/149‑1 (MQ=255)
tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTg > 2:625313/1‑86 (MQ=255)
tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTg < 1:625313/86‑1 (MQ=255)
aTTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGtt < 2:443207/149‑1 (MQ=255)
cAGAAGGCCGGATTTTCTGGTTTCCAGTTG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAGGGCGCAATAGCCAGTTATTCGaa > 1:638070/1‑149 (MQ=255)
cAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGaa > 1:572944/1‑149 (MQ=255)
ccGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGa > 2:449693/1‑114 (MQ=255)
ccGGATTTTCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGa < 1:449693/114‑1 (MQ=255)
aTTTTCTGGTTTCCAGTCG‑CG‑AAAAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGaa < 2:27028/149‑1 (MQ=255)
tCTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTgg < 1:481532/149‑1 (MQ=255)
cTGGTTTCCAGTCG‑CGAA‑AAAAGATAACGAATATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTggg < 2:25930/149‑1 (MQ=255)
tGGTTTCCAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGt > 1:547185/1‑149 (MQ=255)
tGGTTTCCAGTCG‑CG‑AAAAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTCTTCCTCACATGCACACATTGGTAATGAACAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGt < 2:557054/149‑1 (MQ=255)
cAGTCG‑CGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGc < 2:232995/149‑1 (MQ=255)
aaaaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGa > 1:60002/2‑88 (MQ=255)
aaaaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGa < 2:60002/87‑1 (MQ=255)
|||
ATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CG‑C‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGC > NC_000913_3_pae_tpiA/1543884‑1544161
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
