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 I229 R1
|
214 |
17.4 |
943020 |
97.5% |
919444 |
87.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,961,176 |
G→C |
A40G (GCC→GGC) |
cheZ ← |
protein phosphatase CheZ |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,961,176 | 0 | G | C | 100.0%
| 32.6
/ NA
| 12 | A40G (GCC→GGC) | cheZ | protein phosphatase CheZ |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (7/5); total (7/5) |
GCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTGAAT > NZ_CP009273/1961089‑1961260
|
gcCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGccc < 1:301392/90‑1 (MQ=255)
gcCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGccc < 1:419999/90‑1 (MQ=255)
cGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGa > 1:316891/1‑90 (MQ=255)
cGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGa > 2:437910/1‑90 (MQ=255)
gTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCa < 1:187287/59‑1 (MQ=255)
gTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCa > 2:187287/1‑59 (MQ=255)
aCAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATAc < 2:233430/90‑1 (MQ=255)
cAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATAcg > 1:129221/1‑90 (MQ=255)
cAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCACCCCCAGTTCCCGCAAACTGTCGCGCAGCATAcg > 2:393838/1‑90 (MQ=255)
gATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCa > 2:119008/1‑90 (MQ=255)
aTCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAg < 2:126313/90‑1 (MQ=255)
tCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATg > 2:433837/1‑90 (MQ=255)
ttCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGc < 1:132548/90‑1 (MQ=255)
cAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTGAAt < 2:345097/90‑1 (MQ=255)
|
GCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTGAAT > NZ_CP009273/1961089‑1961260
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ 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
GTTCAGCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTGAATGCTCG > NZ_CP009273/1961082‑1961265
|
GTTCAGCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGA > SRR3722113.320000/1‑100 (MQ=60)
cttagtctcgtgggctcggagatgtgtataagagacagACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATC < SRR3722113.127477/62‑1 (MQ=60)
TCAGCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATC < SRR3722113.275573/100‑1 (MQ=60)
CAGCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCC < SRR3722113.49588/100‑1 (MQ=60)
GCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCC < SRR3722113.304258/100‑1 (MQ=60)
GCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCC < SRR3722113.424436/100‑1 (MQ=60)
ggagatgtgtataagagacagGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTC < SRR3722113.188757/79‑1 (MQ=60)
CAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACG > SRR3722113.130311/1‑100 (MQ=60)
TTCGGCAATGCCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTGAATGCTCG < SRR3722113.133663/100‑1 (MQ=60)
|
GTTCAGCGCCCGCTCCGCAGCCTGGGCGGTCATCTGCACAACATAGTACAAACGATCGCGCGCATCGGGGATGGCTTCCGCCGCTTCGGCAATGGCCTGATCCAGCCCCAGTTCCCGCAAACTGTCGCGCAGCATACGCGTCAGGCTGCCGATGCGCGCAATGATATCGCCAGCTGAATGCTCG > NZ_CP009273/1961082‑1961265
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
