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 |
2,526,050 |
A→G |
T95A (ACC→GCC) |
cysK → |
cysteine synthase A |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,526,050 | 0 | A | G | 90.9%
| 52.7
/ ‑0.8
| 22 | T95A (ACC→GCC) | cysK | cysteine synthase A |
| Reads supporting (aligned to +/- strand): ref base A (1/1); new base G (15/5); total (16/6) |
| Fisher's exact test for biased strand distribution p-value = 4.81e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.65e-01 |
GACCAGCGGTAATACCGGGATTGCACTGGCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAACCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTAAAGGCATGAAAGGCGC > NZ_CP009273/2525971‑2526135
|
gACCAGCGGTAATACCGGGATTGCACTGGCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCATGAGTAt > 2:501082/1‑90 (MQ=255)
aCCAGCGGTAATACCGGGATTGCACTGGCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCATGAGTAtt > 2:496491/1‑90 (MQ=255)
aCCAGCGGTAATACCGGGATTGCACTGGCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCATGAGTAtt > 2:397330/1‑90 (MQ=255)
cGGGATTGCACTGGCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAgct > 1:196158/1‑90 (MQ=255)
cGGGATTGCACTGGCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAACCATGAGTATTGAACGCCGCAAgct > 2:665789/1‑90 (MQ=255)
gggATTGCACTGGCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAgctg > 1:56827/1‑90 (MQ=255)
ggCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCa < 2:678534/56‑1 (MQ=255)
ggCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCa > 1:678534/1‑56 (MQ=255)
cTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCAGGAGGATTGAACGCCGCAAGCTGCCGAAAGCGTTAgg > 1:420550/1‑90 (MQ=255)
aTGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTg > 1:635826/1‑90 (MQ=255)
aTGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTg > 2:338940/1‑90 (MQ=255)
gCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAAc > 2:249968/1‑90 (MQ=255)
gCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAAc > 2:710482/1‑90 (MQ=255)
gCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAAc > 1:230409/1‑90 (MQ=255)
ttACAAACTCACCCTGACCATGCCAGAAACCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGa < 2:275691/90‑1 (MQ=255)
tACAAACTCACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGaa < 1:710482/90‑1 (MQ=255)
tACAAACTCACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGaa < 1:338940/90‑1 (MQ=255)
tCACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTa > 2:290677/1‑90 (MQ=255)
cACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTaa > 1:408371/1‑90 (MQ=255)
aTGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGATGGAAGGTGCTAAAGGCATGaaa < 1:516325/90‑1 (MQ=255)
aTGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGATGGAAGGTGCTAAAGGCATGaaa > 2:516325/1‑90 (MQ=255)
aGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTAAAGGCATGAAAGgcgc < 1:454267/90‑1 (MQ=255)
|
GACCAGCGGTAATACCGGGATTGCACTGGCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAACCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTAAAGGCATGAAAGGCGC > NZ_CP009273/2525971‑2526135
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 30 ≤ 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
GCGTTGAACTGGTTGAACCGACCAGCGGTAATACCGGGATTGCACTGGCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAACCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTAAAGGCATGAAAGGCGCAATCCAAAAA > NZ_CP009273/2525952‑2526145
|
GCGTTGAACTGGTTGAACCGACCAGCGGTAATACCGGGATTGCACTGGCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGC > SRR3722112.210811/1‑100 (MQ=60)
AACTGGTTGAACCGACCAGCGGTAATACCGGGATTGCACTGGCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCATGAG < SRR3722112.241122/100‑1 (MQ=60)
GCGGTAATACCGGGATTGCACTGGCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCT > SRR3722112.198551/1‑100 (MQ=60)
CGGTAATACCGGGATTGCACTGGCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTG > SRR3722112.57523/1‑100 (MQ=60)
GGATTGCACTGGCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCATGAGTATTGActgtctcttatacacatctgacgc > SRR3722112.689136/1‑76 (MQ=60)
TTGCACTGGCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCAGGAGGATTGAACGCCGCAAGCTGCCGAAAGCGTTAGG > SRR3722112.426129/1‑100 (MQ=60)
GCACTGGCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTG > SRR3722112.645694/1‑100 (MQ=60)
GGCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAAC > SRR3722112.233174/1‑100 (MQ=60)
GTTACAAACTCACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTAA > SRR3722112.413771/1‑100 (MQ=60)
TACAAACTCACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTAAAG < SRR3722112.343109/100‑1 (MQ=60)
TACAAACTCACCCTGACCATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTAAAG < SRR3722112.721591/100‑1 (MQ=60)
ATGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGATGGAAGGTGCTAAAGGCATGAAAGGCGCAATCC < SRR3722112.523893/100‑1 (MQ=60)
TGCCAGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTAAAGGCATGAAAGGCGCAATCCA > SRR3722112.681638/1‑100 (MQ=60)
AGAAGCCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTAAAGGCATGAAAGGCGCAATCCAAAAA < SRR3722112.460653/100‑1 (MQ=60)
|
GCGTTGAACTGGTTGAACCGACCAGCGGTAATACCGGGATTGCACTGGCCTATGTAGCTGCCGCTCGCGGTTACAAACTCACCCTGACCATGCCAGAAACCATGAGTATTGAACGCCGCAAGCTGCTGAAAGCGTTAGGTGCAAACCTGGTGCTGACGGAAGGTGCTAAAGGCATGAAAGGCGCAATCCAAAAA > NZ_CP009273/2525952‑2526145
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
