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 |
|
A15 F8 I1 R1
|
16 |
40.3 |
1420662 |
94.4% |
1341104 |
140.4 |
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 | 80.0%
| 82.3
/ 16.6
| 30 | coding (40/1389 nt) | narU | nitrate/nitrite transporter |
| Reads supporting (aligned to +/- strand): ref base . (5/1); new base A (13/11); total (18/12) |
| Fisher's exact test for biased strand distribution p-value = 3.58e-01 |
| 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 | 100.0%
| 99.5
/ NA
| 30 | L13F (TTG→TTT) | narU | nitrate/nitrite transporter |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (18/12); total (18/12) |
TTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CG‑C‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAA > NC_000913_3_pae_tpiA/1543879‑1544170
|||
ttGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTCTTATCTAAAGAGGCCGGATTTTCTGGTTTCCAGTCG‑CG‑A‑aa‑aaa < 1:529581/149‑2 (MQ=255)
ttAACGGTAACTGCTCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGAGTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AA‑AAGATAAc < 1:195362/149‑1 (MQ=255)
tGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CG‑AAAA‑AAGATAACGACTATTTTtc > 2:91856/1‑149 (MQ=255)
cgcTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CG‑A‑AACAAGATAACAACTATTTTtctc > 2:503215/1‑149 (MQ=255)
aaTAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AA‑AAGATAACGACTATTTTTCTCAtttt < 2:602100/149‑1 (MQ=255)
cAGAAACAGAAGGCAAGAAGTAGACAACTGACCGATATGCAGAGATTTCTGCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTAAAAAAAA‑AAAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCa < 2:277114/149‑1 (MQ=255)
aGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCat > 2:177622/1‑149 (MQ=255)
aaGGCAAGAAGTAGACAACTGCCTGATATCCAGAGATTCTTACCAGGCATTTTTACTACTCGATAGATCGGGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AA‑AAGATAACGACTATTTTTCTCGTTTTGGAGTGACATATTGTTcc > 1:699322/1‑149 (MQ=255)
gCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTGCGAGCAATATGTTTTCCTTTATTTTCCCAGCAGGCCGGATTTTATGGTTTCCAGTCGCCA‑A‑AA‑AAGATAACAACTATCTTTTTCATGTTACAGTCCAATATACTTcccac > 2:294922/1‑146 (MQ=255)
aagaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTCTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTACCAGTCG‑CGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCGcaca > 1:602401/1‑149 (MQ=255)
aggaGACAACTGACTGATATGCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTAG‑CGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGca < 2:89150/146‑1 (MQ=255)
aCAACTGACTTAGATCCAGAGATTTCTTCGAGGAATATGTTTTCCTTTATTTGCCCAGAAGGCCGGATTTTCTGGTTTACAGTAG‑CGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACAt < 2:235307/149‑1 (MQ=255)
gactgaTATCCAGAGATTTCTTCGAGCAATATGTTTACCTTTAATTTCCCAGAAGGACGGATTTTCTGGTATACAAAAG‑AAAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTaa < 2:326518/149‑1 (MQ=255)
tCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaaaaa < 1:97853/149‑1 (MQ=255)
tCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaaaaa > 1:482410/1‑149 (MQ=255)
cAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCCCACATTGGTAATGaaaaaaaa > 1:677444/1‑148 (MQ=255)
ttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTg < 2:265788/125‑1 (MQ=255)
ttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CG‑AAAA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTg > 1:265788/1‑125 (MQ=255)
ttcGAGCAATATGTTGTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATAGGTAATGAAAAAAAGACAAAACACg > 2:546161/1‑149 (MQ=255)
ccTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGc < 2:482410/149‑1 (MQ=255)
cTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGcc > 2:302335/1‑149 (MQ=255)
cTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGcc > 2:484367/1‑149 (MQ=255)
tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCa > 2:588061/1‑149 (MQ=255)
tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCa > 1:190391/1‑149 (MQ=255)
tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCa < 1:177622/149‑1 (MQ=255)
ttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CG‑AAAA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGAAAAAACCCGAGATAAGGCGCCATAACCat > 2:321088/1‑148 (MQ=255)
aGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAAt > 2:414222/1‑149 (MQ=255)
aGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AA‑AAGATAACGACTATTTTTCTCATTCTGCAGTGCCATATTGTTCCTCACACGCACACATTGGAAATGAAAAAAAGATAAAACCTGAGGTAAGGCTCAATAGCCAGTTATTAGAAt > 2:244222/1‑149 (MQ=255)
gAAGGCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGACTCGGGTGGGAAGACAAAACACGAGGTAGGACGCAATAGCCAGTTATTAGAAtt > 1:520976/1‑149 (MQ=255)
ggCCGGATTTTCTGGTTTCCAGTCG‑CGAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAg < 1:414222/149‑1 (MQ=255)
aaaa‑aaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGaa < 1:302335/147‑1 (MQ=255)
aaa‑aaGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGaaa < 1:484367/148‑1 (MQ=255)
|||
TTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CG‑C‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGATTGAAA > NC_000913_3_pae_tpiA/1543879‑1544170
|
| 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
