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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
601,986 |
A→G |
F285S (TTC→TCC) |
ybdK ← |
YbdK family carboxylate‑amine ligase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 601,986 | 0 | A | G | 100.0%
| 45.2
/ NA
| 15 | F285S (TTC→TCC) | ybdK | YbdK family carboxylate‑amine ligase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (8/7); total (8/7) |
CAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGAAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCC > NZ_CP009273/601904‑602066
|
cAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGtt < 1:110983/90‑1 (MQ=255)
cAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGtt < 2:404484/90‑1 (MQ=255)
ttAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATAcagca < 2:203410/90‑1 (MQ=255)
ttAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATAcagca > 2:85390/1‑90 (MQ=255)
cGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTa < 1:331884/90‑1 (MQ=255)
gtgtGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGt > 2:78013/1‑90 (MQ=255)
tgCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTa > 2:13280/1‑90 (MQ=255)
gCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTaa > 1:225962/1‑90 (MQ=255)
cGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGc > 2:192400/1‑90 (MQ=255)
gTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGt > 2:150992/1‑90 (MQ=255)
cAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAAcc < 2:21449/90‑1 (MQ=255)
cATTGCGACTGGCCTGGGAACGGTTGAATTTATACACCAGGTATTCTTATTCCTGTTGGTTAAGCCGGCGTTCCGTCAGTAACCAGTgcg > 1:264943/1‑88 (MQ=255)
tAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCg > 1:261139/1‑90 (MQ=255)
aGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCgg < 2:580223/90‑1 (MQ=255)
cAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGcc < 1:23398/90‑1 (MQ=255)
|
CAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGAAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCC > NZ_CP009273/601904‑602066
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 34 ≤ 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
TTTTCCAGCAATCGCAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGAAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCCTGAATTAATCCCGC > NZ_CP009273/601890‑602080
|
agcgtcagatgtgtataagagacagCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAAC < SRR3722111.491088/75‑1 (MQ=60)
CAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATAC < SRR3722111.112377/100‑1 (MQ=60)
CGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCC < SRR3722111.336327/100‑1 (MQ=60)
TCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAA > SRR3722111.228691/1‑100 (MQ=60)
CCTTCAAGCCCATTGCGACTGGCCTGGGAACGGTTGAATTTATACACCAGGTATTCTTATTCCTGTTGGTTAAGCCGGCGTTCCGTCAGTAACCAGTGCG > SRR3722111.268111/1‑100 (MQ=48)
TTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCG > SRR3722111.264211/1‑100 (MQ=60)
CAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCCTGAATTAATC < SRR3722111.23688/100‑1 (MQ=60)
GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCCTGAATTAATCCC > SRR3722111.374003/1‑100 (MQ=60)
CCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCCTGAATctgtctctt > SRR3722111.506054/1‑91 (MQ=60)
|
TTTTCCAGCAATCGCAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGAAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCCTGAATTAATCCCGC > NZ_CP009273/601890‑602080
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
