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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
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%
| 89.1
/ NA
| 27 | T250P (ACC→CCC) | hcaR | DNA‑binding transcriptional regulator HcaR |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (9/18); total (9/18) |
TCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTT > NZ_CP009273/2661430‑2661590
|
tctcCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAattat < 1:578303/90‑1 (MQ=255)
ccccTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCa > 2:35229/1‑90 (MQ=255)
tttCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCAtata > 1:397635/1‑90 (MQ=255)
ttcttcCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATaa > 2:172671/1‑90 (MQ=255)
tcttcCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAAc < 2:42850/90‑1 (MQ=255)
cttcCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAAcc > 2:637986/1‑90 (MQ=255)
ttcCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCg < 2:148954/90‑1 (MQ=255)
ttcCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCg < 2:326592/90‑1 (MQ=255)
gCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGccc < 2:496831/90‑1 (MQ=255)
gCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGccc < 2:397635/90‑1 (MQ=255)
cAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCa < 2:73407/90‑1 (MQ=255)
tGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGcc > 1:590428/1‑90 (MQ=255)
aaGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCa < 1:172671/90‑1 (MQ=255)
tttCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCccacc < 1:203020/90‑1 (MQ=255)
tttCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCccacc < 2:371097/90‑1 (MQ=255)
tttCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCccacc < 1:577124/90‑1 (MQ=255)
ggCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGAtt < 2:111832/90‑1 (MQ=255)
ggCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGAtt > 1:706912/1‑90 (MQ=255)
gCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCccacc < 2:314499/84‑1 (MQ=255)
gCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCccacc > 1:314499/1‑84 (MQ=255)
aaTGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGa > 2:250135/1‑62 (MQ=255)
aaTGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGa < 1:250135/62‑1 (MQ=255)
aaTGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCAt < 2:175154/90‑1 (MQ=255)
ggACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTc < 2:354101/90‑1 (MQ=255)
ggACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTc < 2:460185/90‑1 (MQ=255)
aaaaCAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGa < 2:461959/90‑1 (MQ=255)
tGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGtt > 2:61222/1‑90 (MQ=255)
|
TCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTT > NZ_CP009273/2661430‑2661590
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTTGCCACCTGGACGATAT > NZ_CP009273/2661427‑2661606
|
TCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATA > SRR3722112.402862/1‑100 (MQ=60)
TCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACC < SRR3722112.587130/100‑1 (MQ=60)
AGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCC > SRR3722112.599442/1‑100 (MQ=60)
gatgtgtataagagacagCATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCC < SRR3722112.253092/82‑1 (MQ=60)
AAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAG < SRR3722112.174795/100‑1 (MQ=60)
GCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATT > SRR3722112.717962/1‑100 (MQ=60)
CACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTC > SRR3722112.318116/1‑100 (MQ=60)
TTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGG < SRR3722112.205485/100‑1 (MQ=60)
TTTCCGGCAATGGGACGAAAAACAACCTGTCCGGGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGG < SRR3722112.585935/100‑1 (MQ=60)
GGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTTGCCACCTGGACGATAT < SRR3722112.640095/100‑1 (MQ=60)
GGATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTTGCCACCTGGACGATAT < SRR3722112.647898/100‑1 (MQ=60)
|
TCATCTCCCCTTTCTTCCACGCCATCAGTAAAGCAATGGAAGGCACATTTCCGGCAATGGGACGAAAAACAACCTGTCCGGTATTAAAATTATTCATATAACCGGGTATCAAAGTGACGCCCAGCCCCATGCCCACCAGATTCATGGTCACCAGAATATTCGTTGCCACCTGGACGATAT > NZ_CP009273/2661427‑2661606
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
