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 I207 R1
|
218 |
45.0 |
2482936 |
97.1% |
2410930 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,661,508 |
T→G |
T250P (ACC→CCC) |
hcaR ← |
DNA‑binding transcriptional regulator HcaR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,661,508 | 0 | T | G | 100.0%
| 118.6
/ NA
| 35 | T250P (ACC→CCC) | hcaR | DNA‑binding transcriptional regulator HcaR |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (14/21); total (14/21) |
CGGCTTCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTT > NZ_CP009273/2661422‑2661590
|
cGGCTTCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGAtt < 1:46346/90‑1 (MQ=255)
gCTTCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTaa > 1:1228720/1‑90 (MQ=255)
tctcCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAattat < 2:91501/90‑1 (MQ=255)
tcttcCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAAc < 2:716435/90‑1 (MQ=255)
ttcCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCg < 1:1183037/90‑1 (MQ=255)
ttcCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCg < 2:907922/90‑1 (MQ=255)
ccACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCggg > 1:103496/1‑90 (MQ=255)
cGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTAt < 2:488924/90‑1 (MQ=255)
ccATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCa > 2:623665/1‑90 (MQ=255)
aGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTg < 2:306795/90‑1 (MQ=255)
gTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGa < 1:698140/90‑1 (MQ=255)
cAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCa < 2:560434/90‑1 (MQ=255)
cAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCa < 2:543319/90‑1 (MQ=255)
aTGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGc > 2:686983/1‑90 (MQ=255)
aTGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGc > 1:205006/1‑90 (MQ=255)
aTGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGc > 1:508437/1‑90 (MQ=255)
aTGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGc > 1:1219221/1‑90 (MQ=255)
aTGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGc > 1:1149848/1‑90 (MQ=255)
ggAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGccc > 2:988452/1‑90 (MQ=255)
gCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGc > 1:35520/1‑90 (MQ=255)
tttCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCccacc < 1:917490/90‑1 (MQ=255)
tttCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCccacc < 1:864921/90‑1 (MQ=255)
ttCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCccacca < 2:1149848/90‑1 (MQ=255)
ggCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGAtt < 1:988452/90‑1 (MQ=255)
aTGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATg > 2:429668/1‑90 (MQ=255)
tGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATgg < 1:388956/90‑1 (MQ=255)
ggACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTc < 2:498764/90‑1 (MQ=255)
ggACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTc < 1:442578/90‑1 (MQ=255)
ggACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCCGGTATCAAAGTGACGACCAGCCCCATGCCCACCAGATTCATggcc < 2:674348/90‑3 (MQ=255)
ggACGAAAAACAACCGGTCCGGGATTAAAATTACTCATATAACCGGGTATCAAAGTGACGTCCAGCCCCATGCCCACGAGATTCATGGTc < 1:846984/90‑1 (MQ=255)
cGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCAcc > 2:1215306/1‑90 (MQ=255)
cGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCAcc < 1:1192495/90‑1 (MQ=255)
aacCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATAtt < 1:686983/90‑1 (MQ=255)
acCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTc > 1:1172027/1‑90 (MQ=255)
tGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGtt > 1:867748/1‑90 (MQ=255)
|
CGGCTTCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTT > NZ_CP009273/2661422‑2661590
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ 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
CGTAATGCCGGCTTCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTTGCCACCTGGAC > NZ_CP009273/2661414‑2661601
|
CGTAATGCCGGCTTCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAA > SRR3722089.1247394/1‑100 (MQ=60)
AATGCCGGCTTCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAAT < SRR3722089.882068/100‑1 (MQ=60)
CGGCTTCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTC < SRR3722089.46931/100‑1 (MQ=60)
CCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGG > SRR3722089.104776/1‑100 (MQ=60)
CCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAActgtctcttatacacatct > SRR3722089.597942/1‑81 (MQ=60)
TTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAG < SRR3722089.1201049/100‑1 (MQ=60)
CAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGC > SRR3722089.1167353/1‑100 (MQ=60)
CAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGC > SRR3722089.1237770/1‑100 (MQ=60)
CAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGC > SRR3722089.207596/1‑100 (MQ=60)
CAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGC > SRR3722089.514426/1‑100 (MQ=60)
GTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCC < SRR3722089.707243/100‑1 (MQ=60)
GCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGC > SRR3722089.35965/1‑100 (MQ=60)
TTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGG < SRR3722089.930863/100‑1 (MQ=60)
TTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGG < SRR3722089.877303/100‑1 (MQ=60)
GGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACC < SRR3722089.1003112/100‑1 (MQ=60)
TGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAAT < SRR3722089.393695/100‑1 (MQ=60)
GGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATAT < SRR3722089.447883/100‑1 (MQ=60)
GGACGAAAAACAACCGGTCCGGGATTAAAATTACTCATATAACCGGGTATCAAAGTGACGTCCAGCCCCATGCCCACGAGATTCATGGTCACAAGAATAT < SRR3722089.859032/100‑1 (MQ=60)
ACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTC > SRR3722089.1189866/1‑100 (MQ=60)
CGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCG < SRR3722089.1210624/100‑1 (MQ=60)
AAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTT > SRR3722089.880187/1‑100 (MQ=60)
AACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTTGCCACC < SRR3722089.695922/100‑1 (MQ=60)
GTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTTGCCACCTGGAC > SRR3722089.124382/1‑100 (MQ=60)
|
CGTAATGCCGGCTTCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTTGCCACCTGGAC > NZ_CP009273/2661414‑2661601
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
