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 I225 R1
|
227 |
21.4 |
1179702 |
97.1% |
1145490 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,122,267 |
A→C |
S35A (TCG→GCG) |
wcaF ← |
colanic acid biosynthesis acetyltransferase WcaF |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,122,267 | 0 | A | C | 100.0%
| 56.0
/ NA
| 18 | S35A (TCG→GCG) | wcaF | colanic acid biosynthesis acetyltransferase WcaF |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (7/11); total (7/11) |
CGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAA > NZ_CP009273/2122184‑2122352
|
cggacgAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGc > 1:530764/1‑90 (MQ=255)
tAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATAttg < 1:201218/90‑1 (MQ=255)
tAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATAttg < 1:378754/90‑1 (MQ=255)
aCGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGcc < 1:17583/90‑1 (MQ=255)
gTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTg > 1:467773/1‑90 (MQ=255)
ttttttCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGt > 1:359850/1‑90 (MQ=255)
cTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGccc < 2:157547/90‑1 (MQ=255)
cTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGccc < 2:49612/90‑1 (MQ=255)
cTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGccc < 2:378772/90‑1 (MQ=255)
ccGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGc < 1:276534/90‑1 (MQ=255)
ccGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGc < 2:81431/90‑1 (MQ=255)
aataaAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGcc > 2:373829/1‑57 (MQ=255)
aataaAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGcc < 1:373829/57‑1 (MQ=255)
aataaAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCg > 2:492384/1‑90 (MQ=255)
cccGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGcccc < 2:389863/90‑1 (MQ=255)
ggCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAAcc < 1:556502/73‑1 (MQ=255)
ggCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAAcc > 2:556502/1‑73 (MQ=255)
ggCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGaaa > 2:3726/1‑90 (MQ=255)
|
CGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCGAGAAA > NZ_CP009273/2122184‑2122352
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ 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
TTTTTACTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCAC > NZ_CP009273/2122174‑2122345
|
TTTTTACTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGC > SRR3722109.538842/1‑100 (MQ=60)
GAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTG > SRR3722109.474810/1‑100 (MQ=60)
AATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGT > SRR3722109.364814/1‑100 (MQ=60)
TAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTAC < SRR3722109.203657/100‑1 (MQ=60)
TAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTAC < SRR3722109.384119/100‑1 (MQ=60)
cgtcagatgtgtataagagacagGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCC < SRR3722109.379103/77‑1 (MQ=60)
ACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCC < SRR3722109.17810/100‑1 (MQ=60)
CCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAG < SRR3722109.280010/100‑1 (MQ=60)
gagacagCAATACTTGTGGCGCCCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCAC < SRR3722109.564948/93‑1 (MQ=60)
|
TTTTTACTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCAC > NZ_CP009273/2122174‑2122345
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
