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 I211 R1
|
223 |
18.0 |
1007644 |
96.3% |
970361 |
85.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,102,646 |
T→C |
G140G (GGA→GGG) |
wzx ← |
O16 family O‑antigen flippase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,102,646 | 0 | T | C | 100.0%
| 74.4
/ NA
| 23 | G140G (GGA→GGG) | wzx | O16 family O‑antigen flippase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (11/12); total (11/12) |
TTTGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTTCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTA > NZ_CP009273/2102560‑2102727
|
tttGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTcccc < 1:358540/90‑1 (MQ=255)
ttGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCt > 1:164983/1‑90 (MQ=255)
gtgtTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGa > 2:476882/1‑90 (MQ=255)
ttCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAAc < 1:237198/90‑1 (MQ=255)
ttCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAAc < 2:422897/90‑1 (MQ=255)
acaAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGc < 2:295081/90‑1 (MQ=255)
aaaaaaaTAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGc < 1:291211/88‑1 (MQ=255)
tAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGaa > 2:46422/1‑71 (MQ=255)
tAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGaa < 1:46422/71‑1 (MQ=255)
gCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGCAGATTAAATTCCCGACt > 2:371320/1‑90 (MQ=255)
cAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTaa > 1:272381/1‑90 (MQ=255)
cAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTaa > 2:277396/1‑90 (MQ=255)
cGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCa < 2:350324/90‑1 (MQ=255)
ggATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAgg < 1:406962/90‑1 (MQ=255)
ctactTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGc < 1:33613/45‑1 (MQ=255)
ctactTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGc > 2:33613/1‑45 (MQ=255)
ctactTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGAc > 1:324415/1‑90 (MQ=255)
ctTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCat < 1:293470/90‑1 (MQ=255)
tAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCatat > 2:41526/1‑90 (MQ=255)
cAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTAc < 1:383538/90‑1 (MQ=255)
aGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACg > 2:226011/1‑90 (MQ=255)
aGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACg > 2:310601/1‑90 (MQ=255)
ccATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGc < 1:73380/90‑1 (MQ=255)
tcatttTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCt < 1:28669/90‑1 (MQ=255)
ttttctttccCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTta < 1:8282/90‑1 (MQ=255)
ttttctttccCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTta < 1:171831/90‑1 (MQ=255)
|
TTTGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTTCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTA > NZ_CP009273/2102560‑2102727
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ 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
ATATCTGACTTTGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTTCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTATATTCAGGAA > NZ_CP009273/2102551‑2102737
|
ATATCTGACTTTGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCT > SRR3722094.167285/1‑100 (MQ=60)
CTGACTTTGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAA < SRR3722094.459130/100‑1 (MQ=60)
TTTGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCC < SRR3722094.364544/100‑1 (MQ=60)
aagagacagAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGAT < SRR3722094.47075/91‑1 (MQ=60)
TTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAG < SRR3722094.240562/100‑1 (MQ=60)
ggtcgtcggcagcgtcagatgtgtataagagacaGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGT < SRR3722094.34086/66‑1 (MQ=60)
AAAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGT < SRR3722094.295602/100‑1 (MQ=60)
GGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAA > SRR3722094.276451/1‑100 (MQ=60)
GGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGAC > SRR3722094.329653/1‑100 (MQ=60)
GGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGAC < SRR3722094.414017/100‑1 (MQ=60)
CTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGG < SRR3722094.297898/100‑1 (MQ=60)
CAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTG < SRR3722094.390099/100‑1 (MQ=60)
CCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTA < SRR3722094.74423/100‑1 (MQ=60)
TCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTATATTC < SRR3722094.29089/100‑1 (MQ=60)
TTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTATATTCAGGAA < SRR3722094.174226/100‑1 (MQ=60)
TTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTATATTCAGGAA < SRR3722094.8411/100‑1 (MQ=60)
|
ATATCTGACTTTGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTTCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTATATTCAGGAA > NZ_CP009273/2102551‑2102737
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
