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 |
4,543,103 |
A→G |
E129G (GAA→GGA) |
uxuB → |
fructuronate reductase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,543,103 | 0 | A | G | 95.7%
| 67.4
/ ‑5.0
| 23 | E129G (GAA→GGA) | uxuB | fructuronate reductase |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base G (9/13); total (9/14) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGAAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTGC > NZ_CP009273/4543030‑4543187
|
aTCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAg > 1:275710/1‑79 (MQ=255)
aTCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAg < 2:275710/79‑1 (MQ=255)
tCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTg < 1:417362/90‑1 (MQ=255)
cGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGa > 1:18384/1‑90 (MQ=255)
cGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGa > 1:55222/1‑90 (MQ=255)
tGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCa < 2:421965/90‑1 (MQ=255)
gAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGc < 2:19886/90‑1 (MQ=255)
aGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCgg < 2:668167/90‑1 (MQ=255)
tctcAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACt < 1:31632/90‑1 (MQ=255)
aCGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCa > 2:188052/1‑74 (MQ=255)
aCGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCa < 1:188052/74‑1 (MQ=255)
aCGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGAtc < 1:506121/90‑1 (MQ=255)
gcgATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGAtctc < 2:530232/90‑1 (MQ=255)
gcgATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGAtctc < 2:534151/90‑1 (MQ=255)
cgATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCa > 2:405778/1‑90 (MQ=255)
tGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATa > 2:627533/1‑90 (MQ=255)
ggCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATaa < 2:658317/90‑1 (MQ=255)
tCCGCAAACGGCGATTGTCTCTCAAACGGTCACGGAAAACGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCt < 1:468401/90‑1 (MQ=255)
ggTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGAc < 2:307817/90‑1 (MQ=255)
ggTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGAc < 2:655307/90‑1 (MQ=255)
cACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTgc > 1:432497/1‑90 (MQ=255)
cACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTgc > 1:318218/1‑90 (MQ=255)
cACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTgc > 2:388172/1‑90 (MQ=255)
|
ATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGAAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTGC > NZ_CP009273/4543030‑4543187
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ 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
GATGAAAGAAGCGCTGCATCCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGAAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTGCGCCGAAGTCCGCGA > NZ_CP009273/4543005‑4543201
|
gacagAAGAAGCGCTGCATCCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGA < SRR3722112.698016/95‑1 (MQ=60)
GCATCCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCC > SRR3722112.278926/1‑100 (MQ=60)
ATCCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGA > SRR3722112.18614/1‑100 (MQ=60)
ATCCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGA > SRR3722112.55903/1‑100 (MQ=60)
TCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAG < SRR3722112.422869/100‑1 (MQ=60)
agacagGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAAC < SRR3722112.190361/94‑1 (MQ=60)
TCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAAT < SRR3722112.32035/100‑1 (MQ=60)
ACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCC < SRR3722112.513486/100‑1 (MQ=60)
TCCGCAAACGGCGATTGTCTCTCAAACGGTCACGGAAAACGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCAC < SRR3722112.475073/100‑1 (MQ=60)
CTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTGC > SRR3722112.321920/1‑100 (MQ=60)
CTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTGC > SRR3722112.438389/1‑100 (MQ=60)
GGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAAAAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTGCGCCGAAGTCCGCGA > SRR3722112.447990/1‑100 (MQ=60)
|
GATGAAAGAAGCGCTGCATCCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGAAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTGCGCCGAAGTCCGCGA > NZ_CP009273/4543005‑4543201
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
