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 |
|
A23 F79 I1 R1
|
20 |
28.5 |
998386 |
94.1% |
939481 |
141.6 |
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 | 88.9%
| 77.2
/ 3.2
| 28 | coding (40/1389 nt) | narU | nitrate/nitrite transporter |
| Reads supporting (aligned to +/- strand): ref base . (1/2); new base A (10/14); total (12/16) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01 |
| * | NC_000913_3_pae_tpiA | 1,544,022 | 0 | C | A | 100.0%
| 85.3
/ NA
| 28 | L13F (TTG→TTT) | narU | nitrate/nitrite transporter |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (12/16); total (12/16) |
ATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑C‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATG‑AAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGAT > NC_000913_3_pae_tpiA/1543884‑1544165
|||
aTTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATaa < 1:204882/149‑1 (MQ=255)
aTTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAATTGCG‑A‑a‑aaaagacat < 2:372569/149‑7 (MQ=255)
ttAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAAc < 2:321454/149‑1 (MQ=255)
aaCTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTAttt < 2:75842/149‑1 (MQ=255)
cgcTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGATTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTtctc > 1:272135/1‑149 (MQ=255)
gcTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCa > 2:419665/1‑149 (MQ=255)
aTAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGTGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTg < 2:381468/149‑1 (MQ=255)
cATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGt < 2:458019/149‑1 (MQ=255)
tcaaGACACAGAAGGCAAGAAGTAGACAACGGACTGATATACAGAGATTTCTTCGAGCAATATGTTTTCATTTATTTTCCCATAAGGCCGAATTATCTGGTTTCGCGAAAAAAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGc < 2:234570/146‑1 (MQ=255)
cacaGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGACGGATTTTCTGGTTTCCAGTCGAGTA‑A‑AAAGATCACGACTATTTTTCTAATTTTGCAGTGCCataat > 1:477589/1‑147 (MQ=255)
gCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAGTCTGTTTTCCTTTATTTTCCCAGAAGGCCGGGTTTTGTGGTTTCCAGTCGCGAA‑A‑AAAGATCACGACTATTTTTCTCATTTTTCAGTGGCATGTTGTTCTTca > 1:82442/1‑149 (MQ=255)
aCAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTCCAGTGCCATATTGTTCCTCACATGCACACAt > 1:383963/1‑149 (MQ=255)
aCAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑AAA‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACAt > 1:383910/1‑149 (MQ=255)
actgactgATATCCAGAGGTTTATTCGAGCAACATGGTGTTCTTTATTTTCCCAGAAGGCCGGATTTTCTTGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACAttag > 2:297730/1‑147 (MQ=255)
ctgactgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGt < 1:435684/149‑1 (MQ=255)
tgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTTTCTTTTGGCAGTGCCATATTGTTCGTCACATGCACACATTgtgcagga > 1:39244/1‑142 (MQ=255)
atatCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGCTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATG‑aaa > 2:247980/1‑149 (MQ=255)
tcAGAGATTTCTTCGAGCAATATGTACACCCTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATG‑aaaaaaa < 2:477589/148‑1 (MQ=255)
ccAGACATTTGTTCCAGCAATATGTTTTCCCTTATTTTCCCAGAAGGCCGTATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATG‑aaaaaaa < 1:260469/149‑1 (MQ=255)
cAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACTTTTGTAATG‑ACAAAAAg > 2:18805/1‑149 (MQ=255)
tGTTTTCTTTTATTTTCCCAGAAGGCCGGATGTTCTGGTTACAGGTCGCT‑A‑AGAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATG‑AAAAAAAGACAAAACACGAGGTAAGgcgc < 1:413919/149‑1 (MQ=255)
tGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATG‑AAAAAAAGACAAAACACGa > 1:464524/1‑139 (MQ=255)
tGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATG‑AAAAAAAGACAAAACACGa < 2:464524/139‑1 (MQ=255)
ttttCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATG‑AAAAAAAGACAAAACACGAGGTAAGGCGCaa > 1:395393/1‑149 (MQ=255)
ttCCTTTATTTCCCCAGAAGGCCGGATTCTCTGGTTTCCAGTCGCTAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCAATAGTGTTCCTCACATGCACACATTGGTAATG‑AAAAAAAGACAAAACACGAGGTAAGGCGCAATa < 2:419937/149‑1 (MQ=255)
tttATTTTCCCAGAAGGCCTGATTTTCTTGTTTCCAGGCGCGAA‑A‑AAAGATAACTACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATG‑AAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCa < 2:182188/149‑1 (MQ=255)
cAGAAGGCCGGGTTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGTCTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATG‑AAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGaa < 2:175920/149‑1 (MQ=255)
ggCCGGATTTTCTGGTTTCCAGTCGCGAA‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATG‑AAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAg < 1:419665/149‑1 (MQ=255)
gcgaaa‑aaaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGAt < 2:108364/144‑1 (MQ=255)
|||
ATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑C‑A‑AAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATG‑AAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGAT > NC_000913_3_pae_tpiA/1543884‑1544165
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
