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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
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%
| 72.7
/ NA
| 23 | S181P (TCC→CCC) | narP | nitrate/nitrite response regulator protein NarP |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (11/12); total (11/12) |
GCGTGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTTCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGC > NZ_CP009273/2284433‑2284589
|
gCGTGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCg > 1:660144/1‑90 (MQ=255)
gCGTGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCg > 1:823754/1‑90 (MQ=255)
cTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAg < 1:708487/90‑1 (MQ=255)
aCGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACa < 2:406490/90‑1 (MQ=255)
gcgcGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGGGCAGACAGTaaa > 2:701142/1‑90 (MQ=255)
gATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATAtt < 1:381821/90‑1 (MQ=255)
aaTGTTGTGGACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATAtt < 2:611856/89‑1 (MQ=255)
cTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAAt > 2:626890/1‑90 (MQ=255)
gCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCg > 1:352658/1‑90 (MQ=255)
cTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGt < 2:680439/90‑1 (MQ=255)
cTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGt < 1:342339/90‑1 (MQ=255)
ggCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTaa < 2:412469/90‑1 (MQ=255)
ggCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTaa < 2:417982/90‑1 (MQ=255)
ggCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTaa < 1:488172/90‑1 (MQ=255)
ggCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTaa < 2:661182/90‑1 (MQ=255)
ggggCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCaa > 2:272365/1‑90 (MQ=255)
cTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTc > 2:228557/1‑90 (MQ=255)
cTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTc > 1:798881/1‑90 (MQ=255)
gATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTggc > 2:129651/1‑90 (MQ=255)
gATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTggc > 2:475489/1‑90 (MQ=255)
gATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTggc > 2:658777/1‑90 (MQ=255)
aTTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTggcg < 1:352855/90‑1 (MQ=255)
tGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTggcggc < 2:352658/90‑1 (MQ=255)
|
GCGTGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTTCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGC > NZ_CP009273/2284433‑2284589
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 32 ≤ 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
GATCCCTTCAGCGTGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTTCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGTTCCTGCAACAACGCGGGG > NZ_CP009273/2284423‑2284618
|
GATCCCTTCAGCGTGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCG > SRR3722079.667000/1‑100 (MQ=60)
GATCCCTTCAGCGTGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCG > SRR3722079.832574/1‑100 (MQ=60)
TCAGCGTGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGAC < SRR3722079.299596/100‑1 (MQ=60)
CTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAG < SRR3722079.716010/100‑1 (MQ=60)
GATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGC < SRR3722079.384930/100‑1 (MQ=60)
TTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCG > SRR3722079.355430/1‑100 (MQ=60)
CTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATG < SRR3722079.345043/100‑1 (MQ=60)
GGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTC < SRR3722079.492459/100‑1 (MQ=60)
GGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTC > SRR3722079.807440/1‑100 (MQ=60)
ATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTC < SRR3722079.355629/100‑1 (MQ=60)
GTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGTTCCTGC > SRR3722079.556938/1‑100 (MQ=60)
agGAATATTTCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGTTCCTGCAAC < SRR3722079.379098/98‑1 (MQ=60)
CCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGTTCCTGCAACAACGCGGGG > SRR3722079.697678/1‑100 (MQ=60)
|
GATCCCTTCAGCGTGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTTCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGTTCCTGCAACAACGCGGGG > NZ_CP009273/2284423‑2284618
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
