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 F28 I1 R1
|
18 |
13.2 |
538532 |
91.0% |
490064 |
126.1 |
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 | 92.9%
| 38.6
/ ‑2.4
| 14 | coding (40/1389 nt) | narU | nitrate/nitrite transporter |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base A (6/7); total (7/7) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.39e-01 |
| * | NC_000913_3_pae_tpiA | 1,544,022 | 0 | C | A | 100.0%
| 41.2
/ NA
| 14 | L13F (TTG→TTT) | narU | nitrate/nitrite transporter |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (7/7); total (7/7) |
TAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑C‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTA > NC_000913_3_pae_tpiA/1543905‑1544140
|||
tAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTAtt < 1:210220/136‑1 (MQ=255)
aGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCAt > 1:192100/1‑136 (MQ=255)
aGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCa < 1:185519/136‑1 (MQ=255)
ctgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATTca > 2:170782/1‑136 (MQ=255)
agaTTTTTTCGACAAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGGTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCCTTTTGCAGTACCTGCGTGTTCCTCACATGCCCACATTGGTaa > 2:179634/1‑136 (MQ=255)
aTTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCAGATTGTTCCTCACATGCACACATTGGTACTg > 2:193402/1‑136 (MQ=255)
ttcttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑AAAAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaa > 2:7720/1‑136 (MQ=255)
gAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAg < 1:7720/136‑1 (MQ=255)
cgagagGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATa < 1:183714/134‑1 (MQ=255)
aGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTca < 1:199196/79‑1 (MQ=255)
aGGCCGGATTTTCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTca > 2:199196/1‑79 (MQ=255)
ttCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTtc > 1:77385/1‑41 (MQ=255)
ttCTGGTTTCCAGTCGCGAA‑AAAAGATAACGACTATTTTtc < 2:77385/41‑1 (MQ=255)
ttGGTTTTCAGTCGCGAA‑AAAAGATAAGGACTATTTTTCTCTTTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTa < 1:170782/135‑1 (MQ=255)
|||
TAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCGCG‑C‑AAAAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTA > NC_000913_3_pae_tpiA/1543905‑1544140
|
| 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
