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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
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 | 87.5%
| 54.5
/ 2.3
| 24 | F285S (TTC→TCC) | ybdK | YbdK family carboxylate‑amine ligase |
| Reads supporting (aligned to +/- strand): ref base A (1/2); new base G (13/8); total (14/10) |
| Fisher's exact test for biased strand distribution p-value = 5.50e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AATCGCAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGAAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCCTG > NZ_CP009273/601899‑602068
|
aaTCGCAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGgaa < 2:831075/90‑1 (MQ=255)
cAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGtt < 2:333181/90‑1 (MQ=255)
cAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGtt < 1:273775/90‑1 (MQ=255)
aTCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAAttt > 1:217606/1‑90 (MQ=255)
gTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGAAACGGTTGAATTTATAcagc > 2:659093/1‑90 (MQ=255)
cgaTCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCtttt < 2:712291/90‑1 (MQ=255)
ccAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGa < 2:438979/90‑1 (MQ=255)
gtgCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGttt > 2:791666/1‑90 (MQ=255)
gtgCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGttt > 1:511052/1‑90 (MQ=255)
gtgCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGttt > 2:343847/1‑90 (MQ=255)
gCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTaa > 1:729384/1‑90 (MQ=255)
cGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGc > 2:681561/1‑90 (MQ=255)
gatgaCGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTc > 1:506569/1‑90 (MQ=255)
gaCGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGt < 2:297884/90‑1 (MQ=255)
cAAGCCCATAGCGACAGGCCTGGAAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAAcc < 1:266494/90‑1 (MQ=255)
aTAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGc > 1:734306/1‑90 (MQ=255)
aGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCgg < 1:214319/90‑1 (MQ=255)
aGCGACAGGCCTGGAAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCgg < 2:606051/90‑1 (MQ=255)
gCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGt < 1:623627/90‑1 (MQ=255)
gACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAg > 1:86966/1‑90 (MQ=255)
gACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAg > 1:277878/1‑90 (MQ=255)
cAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGcc < 2:367643/90‑1 (MQ=255)
cAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGcc > 2:826053/1‑90 (MQ=255)
ggCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCCTg > 2:426051/1‑90 (MQ=255)
ggCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCCTg > 2:28322/1‑90 (MQ=255)
|
AATCGCAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGAAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCCTG > NZ_CP009273/601899‑602068
|
| 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
ATCGCAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGAAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCCTGAATTAATCCCG > NZ_CP009273/601900‑602079
|
ATCGCAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTT > SRR3722079.219458/1‑100 (MQ=60)
CAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATAC < SRR3722079.276065/100‑1 (MQ=60)
GATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTT > SRR3722079.515704/1‑100 (MQ=60)
TCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAA > SRR3722079.737181/1‑100 (MQ=60)
GCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTC > SRR3722079.511168/1‑100 (MQ=60)
CTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGC > SRR3722079.742157/1‑100 (MQ=60)
CAAGCCCATAGCGACAGGCCTGGAAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGT < SRR3722079.268727/100‑1 (MQ=60)
AGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAG > SRR3722079.280197/1‑100 (MQ=60)
AGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAG > SRR3722079.87660/1‑100 (MQ=60)
AGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCCTGAAT < SRR3722079.216147/100‑1 (MQ=60)
GCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCCTGAATT < SRR3722079.629984/100‑1 (MQ=60)
GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCCTGAATTAATCCC > SRR3722079.39879/1‑100 (MQ=60)
GCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCCTGAATTAATCCCG > SRR3722079.452447/1‑100 (MQ=60)
|
ATCGCAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGAAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCCTGAATTAATCCCG > NZ_CP009273/601900‑602079
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
