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 F3 I95 R1
|
196 |
14.2 |
808436 |
96.0% |
776098 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,336,254 |
T→G |
D297A (GAC→GCC) |
fumB ← |
class I fumarate hydratase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,336,254 | 0 | T | G | 100.0%
| 39.8
/ NA
| 13 | D297A (GAC→GCC) | fumB | class I fumarate hydratase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (7/6); total (7/6) |
CTTTAATGTTACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCA > NZ_CP009273/4336168‑4336329
|
cTTTAATGTTACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGt < 2:63010/90‑1 (MQ=255)
tACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGt > 2:136054/1‑90 (MQ=255)
agaCGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTgc < 1:240803/89‑1 (MQ=255)
agaCGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTgc > 2:240803/1‑89 (MQ=255)
cGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTgcgcgc < 2:46675/90‑1 (MQ=255)
cGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTgcgcgc > 1:320448/1‑90 (MQ=255)
aTGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGa > 1:280859/1‑61 (MQ=255)
aTGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGa < 2:280859/61‑1 (MQ=255)
tGACGTGCCAGACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCcagc < 1:210293/90‑1 (MQ=255)
tGACGTGCCAGACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCcagc > 2:210293/1‑90 (MQ=255)
aGACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTGTGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGt > 1:174135/1‑90 (MQ=255)
gACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGtt < 1:210602/90‑1 (MQ=255)
ggATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCa > 1:229238/1‑90 (MQ=255)
|
CTTTAATGTTACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCA > NZ_CP009273/4336168‑4336329
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAGCTGGACATCGCGGAA > NZ_CP009273/4336188‑4336345
|
GAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTGCGCGC > SRR3722235.324981/1‑100 (MQ=60)
GGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCctgtctcttatacacatct > SRR3722235.284711/1‑81 (MQ=60)
GAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGAC < SRR3722235.243864/100‑1 (MQ=60)
GTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTGTGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGT > SRR3722235.176135/1‑100 (MQ=60)
TGACGTGCCAGACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTT < SRR3722235.212887/100‑1 (MQ=60)
CGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCA > SRR3722235.232133/1‑100 (MQ=60)
GACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAGCTGGAC < SRR3722235.213204/100‑1 (MQ=60)
CGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAGCTGGACATCGCGGAA > SRR3722235.57460/1‑100 (MQ=60)
|
GAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAGCTGGACATCGCGGAA > NZ_CP009273/4336188‑4336345
|
| 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: ‑ |
