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 |
|
A1 F2 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,284,519 |
T→C |
S181P (TCC→CCC) |
narP → |
nitrate/nitrite response regulator protein NarP |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,284,519 | 0 | T | C | 100.0%
| 76.5
/ NA
| 22 | S181P (TCC→CCC) | narP | nitrate/nitrite response regulator protein NarP |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (12/10); total (12/10) |
TGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTTCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGT > NZ_CP009273/2284436‑2284600
|
tGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGc < 2:716848/90‑1 (MQ=255)
tGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGc > 2:442474/1‑90 (MQ=255)
cTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAg < 1:154520/90‑1 (MQ=255)
gACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGAc < 2:159229/90‑1 (MQ=255)
gACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGAc < 1:874937/90‑1 (MQ=255)
gAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTa > 1:804592/1‑90 (MQ=255)
tCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTaaa < 2:478773/75‑1 (MQ=255)
tCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTaaa > 1:478773/1‑75 (MQ=255)
gCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATct > 2:524939/1‑90 (MQ=255)
cGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATctgct < 1:50594/90‑1 (MQ=255)
gCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCg > 2:750663/1‑90 (MQ=255)
ggggCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAg > 2:507354/1‑53 (MQ=255)
ggggCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAg < 1:507354/53‑1 (MQ=255)
ggggCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCaa > 2:263063/1‑90 (MQ=255)
aaTAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCa > 2:271902/1‑90 (MQ=255)
aaTAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCa > 2:7604/1‑90 (MQ=255)
cAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTg > 1:116094/1‑90 (MQ=255)
gATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTggc > 1:655144/1‑90 (MQ=255)
aTTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTggcg < 2:108847/90‑1 (MQ=255)
tGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTggcggc < 2:357940/90‑1 (MQ=255)
cTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGccac < 1:263063/90‑1 (MQ=255)
tGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGt > 1:73592/1‑90 (MQ=255)
|
TGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTTCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGT > NZ_CP009273/2284436‑2284600
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CCCTTCAGCGTGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTTCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGTTCCTGCAACAACGCGG > NZ_CP009273/2284426‑2284616
|
CCCTTCAGCGTGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGC < SRR3722072.186380/100‑1 (MQ=60)
CTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAG < SRR3722072.157240/100‑1 (MQ=60)
GACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTA > SRR3722072.818632/1‑100 (MQ=60)
GACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTA < SRR3722072.890006/100‑1 (MQ=60)
gggctcggagatgtgtataagagacaGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACA < SRR3722072.516491/74‑1 (MQ=60)
AGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCtgtc > SRR3722072.487467/1‑96 (MQ=60)
CGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTC < SRR3722072.51519/100‑1 (MQ=60)
atcggacgtctcgtgggctcggagatgtgtataagagacagGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATG < SRR3722072.208303/59‑1 (MQ=60)
GTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTG > SRR3722072.118227/1‑100 (MQ=60)
CAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGC > SRR3722072.666838/1‑100 (MQ=60)
GCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGT > SRR3722072.74962/1‑100 (MQ=60)
CTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGTTC < SRR3722072.267528/100‑1 (MQ=60)
GTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGTTCCTGC > SRR3722072.760756/1‑100 (MQ=60)
GAATATTCCCGAGCAGACAGTAAAAGTACATATTCtgtctcttatacacatctccgagcccacgagacgtccgattatctcgtatgccgtcttctgcttg > SRR3722072.304790/1‑35 (MQ=59)
GAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGTTCCTGCAACAA > SRR3722072.604262/1‑100 (MQ=60)
TTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCctgtctcttatacacatctccgagcc > SRR3722072.639764/1‑74 (MQ=60)
|
CCCTTCAGCGTGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTTCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGTTCCTGCAACAACGCGG > NZ_CP009273/2284426‑2284616
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
