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 |
1,065,426 |
T→G |
T129P (ACC→CCC) |
rutF ← |
pyrimidine utilization flavin reductase protein F |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,065,426 | 0 | T | G | 100.0%
| 46.6
/ NA
| 15 | T129P (ACC→CCC) | rutF | pyrimidine utilization flavin reductase protein F |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (12/3); total (12/3) |
ATAACTGCGATCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGTGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGCCTCTTCCAGTTGCGGGCATCCGGTCACCC > NZ_CP009273/1065343‑1065503
|
aTAACTGCGATCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGAc < 1:231271/90‑1 (MQ=255)
aCTGCGATCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCt > 2:634045/1‑90 (MQ=255)
gCGATCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTcac < 2:391405/90‑1 (MQ=255)
tCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCaccacc < 1:540097/90‑1 (MQ=255)
gCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGc > 2:223489/1‑90 (MQ=255)
tgtggtgtgACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGa > 2:443318/1‑90 (MQ=255)
gtggtgtgACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGaa > 2:323086/1‑90 (MQ=255)
gtgtgACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAAcc > 1:368532/1‑90 (MQ=255)
gtgtgACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAAcc > 2:492891/1‑90 (MQ=255)
aCGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGc > 1:502204/1‑90 (MQ=255)
gATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGCct > 2:95522/1‑90 (MQ=255)
gcAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGCCTCTTCCAGTTGCGGGCATcc > 1:166917/1‑90 (MQ=255)
gAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGCCTCTTCCAGTTGCGGGCATCCGGTCAccc > 1:192109/1‑90 (MQ=255)
gAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGCCTCTTCCAGTTGCGGGCATCCGGTCAccc > 1:295620/1‑90 (MQ=255)
gAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGCCTCTTCCAGTTGCGGGCATCCGGTCAccc > 2:264597/1‑90 (MQ=255)
|
ATAACTGCGATCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGTGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGCCTCTTCCAGTTGCGGGCATCCGGTCACCC > NZ_CP009273/1065343‑1065503
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ 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
GCGCATCAGCGCGTGATAACTGCGATCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGTGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGCCTCTTCCAGTTGCGGGCATCCGGTCACCCCCGTCTGCCAGCGGGC > NZ_CP009273/1065328‑1065519
|
GCGCATCAGCGCGTGATAACTGCGATCGAACCACACCAGCCCGTAGGGCGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGGGGGGG > SRR3722112.72339/1‑100 (MQ=60)
ATAACTGCGATCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACC < SRR3722112.234047/100‑1 (MQ=60)
TCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATAC < SRR3722112.548172/100‑1 (MQ=60)
GTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACC > SRR3722112.373284/1‑100 (MQ=60)
GTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGC > SRR3722112.509487/1‑100 (MQ=60)
CTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGCCTCTTCCAGTTGCGGGCATCC > SRR3722112.168967/1‑100 (MQ=60)
GCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGCCTCTTCCAGTTGCGGGCATCCGGTCACCC > SRR3722112.194460/1‑100 (MQ=60)
GCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGCCTCTTCCAGTTGCGGGCATCCGGTCACCC > SRR3722112.299033/1‑100 (MQ=60)
CGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGCCTCTTCCAGTTGCGGGCATCCGGTCACCCCCGTCTGCCAGCGGGC > SRR3722112.254792/1‑100 (MQ=60)
|
GCGCATCAGCGCGTGATAACTGCGATCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGTGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGCCTCTTCCAGTTGCGGGCATCCGGTCACCCCCGTCTGCCAGCGGGC > NZ_CP009273/1065328‑1065519
|
| 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: ‑ |
