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 F12 I1 R1
|
17 |
33.0 |
1187876 |
93.7% |
1113039 |
142.3 |
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 | 78.3%
| 58.9
/ 14.0
| 23 | coding (40/1389 nt) | narU | nitrate/nitrite transporter |
| Reads supporting (aligned to +/- strand): ref base . (3/2); new base A (8/10); total (11/12) |
| Fisher's exact test for biased strand distribution p-value = 6.40e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.76e-01 |
| * | NC_000913_3_pae_tpiA | 1,544,022 | 0 | C | A | 100.0%
| 74.2
/ NA
| 23 | L13F (TTG→TTT) | narU | nitrate/nitrite transporter |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (11/12); total (11/12) |
ACGGTAACTGCGCTAAATAGCATCCAGACACAGAA‑GGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCGCG‑C‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAAGA > NC_000913_3_pae_tpiA/1543888‑1544172
|||
aCGGTAACTGCGCTAAATAGCATCCAGACACAGAACACCCAGAGGT‑TACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCT‑AGTTGCGAA‑AAAA‑GATAAcagct > 1:295381/1‑146 (MQ=255)
tAAATAGCATCCAGACACAGAA‑GGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCGCG‑AAAAAA‑GATAACGACTATTTTTCTCAttt > 2:105857/1‑150 (MQ=255)
aaTAGCATCCAGACACAGAA‑GGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCGCG‑A‑AAAATGATAACGACTATTTTTCTCATTTTg < 2:500295/150‑1 (MQ=255)
aTCCAGACACAGAA‑GGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTATTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCGCGAA‑AAAA‑GATCACGACTCTTTTTCTCATTTTGCCGTGc > 2:152748/1‑150 (MQ=255)
aGACACAGAA‑GGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCGCGAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCata < 1:105857/150‑1 (MQ=255)
aagaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCGCGAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCa > 2:57497/1‑129 (MQ=255)
aagaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCGCGAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCa < 1:57497/129‑1 (MQ=255)
aagaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCGCGAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACAt < 1:86679/150‑1 (MQ=255)
agaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCGCGAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGcc < 1:211107/133‑1 (MQ=255)
agaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCGCGAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGcc > 2:211107/1‑133 (MQ=255)
agaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCGCGAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATg < 1:152748/150‑1 (MQ=255)
agTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTAA‑AAAAAAAAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGcac < 2:138498/150‑1 (MQ=255)
actgaTATGCAGAGAGTGCTTCGAGCAATATGTTTTCCTTTATTTTCACAGAAGGCCGGATTTTTTGGTTTCCAAAAAAAA‑A‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATg < 2:586261/150‑1 (MQ=255)
actgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCGCGAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATg > 1:354832/1‑150 (MQ=255)
atatCCAGAGCTTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCGCGAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCCTATTGTTCCTCACATGCACACATGGGTAATGaaaa > 1:173139/1‑150 (MQ=255)
ttcaaacAATATGTCTTCCTTTACTTACCAACAAGGCCGGATTTTCTGGTTTCC‑AGTCGCGAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGa < 1:110735/144‑1 (MQ=255)
tttCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCGCGAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATa > 1:357117/1‑150 (MQ=255)
tttCTGGTTTCC‑AGTCGCGAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGc > 1:269593/1‑75 (MQ=255)
tttCTGGTTTCC‑AGTCGCGAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGc < 2:269593/75‑1 (MQ=255)
ttCTGGTTTCC‑AGGCGCGAA‑AAAA‑GATAAAGAATATCATTTTAAATATCCATTTCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGAACTAGCCAGTCATTAGAACTACGGATGCAttcg < 2:568833/150‑3 (MQ=255)
c‑AGTCGCGAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGtt < 1:22870/54‑1 (MQ=255)
c‑AGTCGCG‑AAAAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGtt > 2:22870/1‑54 (MQ=255)
c‑AGTCGCG‑AAAAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCt > 1:431512/1‑150 (MQ=255)
gcgaaaaaa‑GATAACGACTATTTTTTTCATTTTGCAGTGACATATTGTTCCCCACATGCACACATTGGTAAAGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTg < 2:322604/145‑1 (MQ=255)
aaaa‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAAGa < 1:548814/150‑1 (MQ=255)
|||
ACGGTAACTGCGCTAAATAGCATCCAGACACAGAA‑GGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCC‑AGTCGCG‑C‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAAGA > NC_000913_3_pae_tpiA/1543888‑1544172
|
| 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
