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 I210 R1
|
226 |
19.6 |
1130256 |
95.4% |
1078264 |
84.4 |
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%
| 55.8
/ NA
| 18 | S181P (TCC→CCC) | narP | nitrate/nitrite response regulator protein NarP |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (8/10); total (8/10) |
GTGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTTCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGT > NZ_CP009273/2284435‑2284600
|
gTGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAg > 2:213076/1‑90 (MQ=255)
tGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGc < 1:356389/90‑1 (MQ=255)
tGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGc > 1:125629/1‑90 (MQ=255)
tGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGc < 2:281453/90‑1 (MQ=255)
cTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAg > 2:423722/1‑90 (MQ=255)
gACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAACAGAc < 2:365067/90‑1 (MQ=255)
aCGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACa < 2:371598/90‑1 (MQ=255)
gcgcGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTaaa < 1:379007/90‑1 (MQ=255)
gATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATAtt < 1:483414/90‑1 (MQ=255)
ggggCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCaa > 2:55387/1‑90 (MQ=255)
cTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGt > 2:464960/1‑56 (MQ=255)
cTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGt < 1:464960/56‑1 (MQ=255)
cTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTc < 1:342637/90‑1 (MQ=255)
cAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCTCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTg > 2:161510/1‑90 (MQ=255)
aTTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTggcg < 2:125629/90‑1 (MQ=255)
gtgtTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCAtt > 1:295681/1‑90 (MQ=255)
tgtTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCTCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTc < 1:161510/90‑1 (MQ=255)
tGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGt > 1:192208/1‑90 (MQ=255)
|
GTGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTTCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGT > NZ_CP009273/2284435‑2284600
|
| 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
CCCTTCAGCGTGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTTCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGTTCCTGCA > NZ_CP009273/2284426‑2284607
|
CCCTTCAGCGTGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGC > SRR3722092.127753/1‑100 (MQ=60)
TGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAA < SRR3722092.362921/100‑1 (MQ=60)
GCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATT < SRR3722092.386183/100‑1 (MQ=60)
gcgtcagatgtgtataagagacagGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGC < SRR3722092.474163/76‑1 (MQ=60)
GATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGC < SRR3722092.493028/100‑1 (MQ=60)
CTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCG < SRR3722092.348761/100‑1 (MQ=60)
GATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATT > SRR3722092.300863/1‑100 (MQ=60)
GCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGT > SRR3722092.195405/1‑100 (MQ=60)
GTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGTTCCTGC > SRR3722092.306150/1‑100 (MQ=60)
GTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGTTCCTGC > SRR3722092.547918/1‑100 (MQ=60)
TGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCTCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGTTCCTGCA < SRR3722092.164217/100‑1 (MQ=60)
|
CCCTTCAGCGTGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTTCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGTTCCTGCA > NZ_CP009273/2284426‑2284607
|
| 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: ‑ |
