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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
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 | 100.0%
| 147.4
/ NA
| 45 | E129G (GAA→GGA) | uxuB | fructuronate reductase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (22/23); total (22/23) |
CCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGAAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTGC > NZ_CP009273/4543024‑4543187
|
ccGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTAc < 2:776537/90‑1 (MQ=255)
gAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTgc < 2:617934/90‑1 (MQ=255)
tGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGgaaa < 1:699919/72‑1 (MQ=255)
tGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGgaaa > 2:699919/1‑72 (MQ=255)
gCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCgg > 2:1553074/1‑90 (MQ=255)
aGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCgg > 2:1205390/1‑90 (MQ=255)
aGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCgg < 2:703170/90‑1 (MQ=255)
ggTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGt < 2:1324189/90‑1 (MQ=255)
ggTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGt < 2:825435/90‑1 (MQ=255)
aTTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCaa > 2:1083801/1‑90 (MQ=255)
tctcAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACt < 2:868665/90‑1 (MQ=255)
cAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGa < 1:1205390/90‑1 (MQ=255)
cAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGa > 2:1097610/1‑90 (MQ=255)
aaCGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGAt < 2:669098/90‑1 (MQ=255)
aCGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGAtc > 1:1197110/1‑90 (MQ=255)
aCGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGAtc < 2:10346/90‑1 (MQ=255)
aCGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGAtc < 2:1134740/90‑1 (MQ=255)
aCGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGAtc < 1:114895/90‑1 (MQ=255)
aCGCGATGGCGCGTCCGCAAACGGCGATGGGCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGAtc > 2:767779/1‑90 (MQ=255)
cgATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCa > 2:602739/1‑90 (MQ=255)
cgATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTAACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTc > 1:277893/1‑78 (MQ=255)
cgATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTAACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTc < 2:277893/78‑1 (MQ=255)
aTGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAAt > 2:303701/1‑90 (MQ=255)
aTGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAAt < 1:1107688/90‑1 (MQ=255)
tGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATa < 1:1083801/90‑1 (MQ=255)
gcgcGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAAc > 2:314639/1‑90 (MQ=255)
cgTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCg < 2:217594/90‑1 (MQ=255)
gTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGc < 2:1063755/90‑1 (MQ=255)
gTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGc > 2:1056616/1‑90 (MQ=255)
cGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGc < 2:628128/90‑1 (MQ=255)
gCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCAc > 2:1576407/1‑90 (MQ=255)
cGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACg > 1:484441/1‑90 (MQ=255)
gATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGa > 2:1142919/1‑90 (MQ=255)
ctctctAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGa > 2:1572543/1‑90 (MQ=255)
ctctAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATaa > 2:683642/1‑64 (MQ=255)
ctctAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATaa < 1:683642/64‑1 (MQ=255)
ctctAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGaaa > 2:1466607/1‑90 (MQ=255)
ctctAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGaaa > 1:762490/1‑90 (MQ=255)
cGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATa > 1:1307850/1‑57 (MQ=255)
cGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATa < 2:1307850/57‑1 (MQ=255)
ggTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGAc < 1:92763/90‑1 (MQ=255)
ggTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGAc < 1:54364/90‑1 (MQ=255)
ggTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGAc < 1:182154/90‑1 (MQ=255)
ggTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGAc < 1:161726/90‑1 (MQ=255)
gTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACt > 2:1556934/1‑90 (MQ=255)
cACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTgc > 2:598464/1‑90 (MQ=255)
cACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTgc > 2:1405169/1‑90 (MQ=255)
|
CCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGAAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTGC > NZ_CP009273/4543024‑4543187
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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
CGATGAAAGAAGCGCTGCATCCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGAAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTGCGCCGAAGTCCGCGAT > NZ_CP009273/4543004‑4543202
|
CGATGAAAGAAGCGCTGCATCCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGG < SRR3722078.1341527/100‑1 (MQ=60)
CGATGAAAGAAGCGCTGCATCCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGG < SRR3722078.766700/100‑1 (MQ=60)
agagacagCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGC < SRR3722078.708350/92‑1 (MQ=60)
GGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATC > SRR3722078.1215887/1‑100 (MQ=60)
ATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTAACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCT > SRR3722078.281284/1‑100 (MQ=60)
CAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAAC < SRR3722078.1224305/100‑1 (MQ=60)
ACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCC < SRR3722078.116241/100‑1 (MQ=60)
ATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGA < SRR3722078.1124581/100‑1 (MQ=60)
TGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGAT < SRR3722078.1100203/100‑1 (MQ=60)
tgtgtataagagacaGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATC < SRR3722078.691631/85‑1 (MQ=60)
CCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACG > SRR3722078.490198/1‑100 (MQ=60)
GCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAA > SRR3722078.772291/1‑100 (MQ=60)
GTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCtgtctcttatacacatctgacg > SRR3722078.1328719/1‑78 (MQ=60)
CTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCtgtctctt > SRR3722078.1310725/1‑92 (MQ=60)
CTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTGCGC > SRR3722078.460531/1‑100 (MQ=60)
GGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTGCGCCGAAG < SRR3722078.93852/100‑1 (MQ=60)
GGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTGCGCCGAAG < SRR3722078.55012/100‑1 (MQ=60)
GGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTGCGCCGAAG < SRR3722078.184315/100‑1 (MQ=60)
GGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTGCGCCGAAG < SRR3722078.163613/100‑1 (MQ=60)
GTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTGCGCCGAAGT > SRR3722078.1305451/1‑100 (MQ=60)
GTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTGCGCCGAAGT > SRR3722078.1132093/1‑100 (MQ=60)
GGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTGCGCCGAAGTCCGCGA > SRR3722078.489642/1‑100 (MQ=60)
GAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTGCGCCGAAGTCCGCGAT < SRR3722078.741537/100‑1 (MQ=60)
|
CGATGAAAGAAGCGCTGCATCCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGAAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTGCGCCGAAGTCCGCGAT > NZ_CP009273/4543004‑4543202
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
