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 F10 I1 R1
|
17 |
30.2 |
1100966 |
93.3% |
1027201 |
143.3 |
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 | 83.3%
| 44.9
/ 3.8
| 18 | coding (40/1389 nt) | narU | nitrate/nitrite transporter |
| Reads supporting (aligned to +/- strand): ref base . (2/1); new base A (9/6); total (11/7) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| 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 | 94.4%
| 47.3
/ NA
| 18 | L13F (TTG→TTT) | narU | nitrate/nitrite transporter |
| Reads supporting (aligned to +/- strand): ref base C (0/1); new base A (11/6); total (11/7) |
| Fisher's exact test for biased strand distribution p-value = 3.89e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01 |
AGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑C‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGAT > NC_000913_3_pae_tpiA/1543919‑1544165
|||
aGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGAATTCGTCGAGCAATATGGTTTCCTTGATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑A‑AAAAGGATAACGACTATTTTTCTCATTTTGCAGTTCAATATTGtt > 1:162014/1‑149 (MQ=255)
gggCGAGAGGTAGACAAGTGACGGATATCCAGTGATTTCTTCGGGCATGATGGTTTCCTTCTTTTTCCGAGAAGGGCTGTGTTTCTGGTTTCCAGTCGC‑GAC‑AAAA‑GATCACGACTATTTTGCTCATTTTGCAGTGCCATATTGTTCCt < 2:459/148‑1 (MQ=255)
aGGCAAGAAGTAGACAACTGACTGATATCCAGAGTTTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCt < 1:426588/149‑1 (MQ=255)
ctgactgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGt > 1:267863/1‑149 (MQ=255)
ctgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑AAAAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATg < 2:535396/149‑1 (MQ=255)
tgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGCTTTCCAGTCGC‑GAA‑AAAA‑CATAACGCCTATTTTTCTCATTTTGCAGTCCCATATTGTTCCTCACTTGCACACATTCGTAATGa > 2:473839/1‑149 (MQ=255)
atCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGACGTGGCATATTTTTCCTCACATGCACACATTGGTAATGaaaaa > 1:13473/1‑149 (MQ=255)
cAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAg > 1:410647/1‑149 (MQ=255)
atagaTTGCTTCGAGTAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGa < 1:110666/147‑1 (MQ=255)
agagATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGa > 1:305304/1‑149 (MQ=255)
tttCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAAt > 1:4655/1‑149 (MQ=255)
tttATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCa > 1:467762/1‑149 (MQ=255)
tttATTTTCCCAGAAGGCCGGATTTTCTGAAATAACAACGCTA‑A‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATGGCCa > 1:271112/1‑149 (MQ=255)
tttATTTGCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACAAAATAGTAAAGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCa < 1:123914/149‑1 (MQ=255)
cAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACGATGTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGaa > 2:503884/1‑149 (MQ=255)
aGGCCGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTaa < 1:326822/149‑1 (MQ=255)
cGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGAt < 2:410647/149‑1 (MQ=255)
cGGATTTTCTGGTTTCCAGTCGC‑GAA‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGAAAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTacgcat > 2:259846/1‑144 (MQ=255)
ggagaaaaaa‑GAGAACGACTATTTTTCTCGTTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGAt < 2:267863/143‑1 (MQ=255)
|||
AGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGC‑G‑C‑AAAA‑GATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGTGCTGAT > NC_000913_3_pae_tpiA/1543919‑1544165
|
| 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
