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 I230 R1
|
226 |
18.8 |
1048726 |
96.7% |
1014118 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,995,567 |
A→G |
T635A (ACC→GCC) |
xdhA → |
xanthine dehydrogenase molybdenum‑binding subunit XdhA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,995,567 | 0 | A | G | 100.0%
| 107.9
/ NA
| 33 | T635A (ACC→GCC) | xdhA | xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (23/10); total (23/10) |
GAAAGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCACCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGG > NZ_CP009273/2995480‑2995651
|
gAAAGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGcc > 1:232720/1‑90 (MQ=255)
ccATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAAcc > 1:27190/1‑90 (MQ=255)
ccATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAAcc > 2:204873/1‑90 (MQ=255)
aTCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGc < 1:197628/90‑1 (MQ=255)
acccccACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTc < 2:260570/90‑1 (MQ=255)
caccacTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGCTATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCaa < 1:401785/90‑1 (MQ=255)
aCCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTc > 2:110107/1‑90 (MQ=255)
aCCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTc > 2:188279/1‑90 (MQ=255)
gTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCa > 1:433156/1‑90 (MQ=255)
tttGGCTGACCCTTTGTTGTTCTCACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCat < 2:403301/90‑1 (MQ=255)
ttGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCata < 1:156665/90‑1 (MQ=255)
ggCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATAtt > 1:32744/1‑90 (MQ=255)
gTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTa > 2:374922/1‑90 (MQ=255)
tttGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCa > 1:504550/1‑90 (MQ=255)
ttgttgATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCAc > 1:374702/1‑90 (MQ=255)
ttgttgATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCAc > 1:97558/1‑90 (MQ=255)
gATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCActgctg < 2:194297/90‑1 (MQ=255)
tCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGc > 2:82468/1‑90 (MQ=255)
tCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGc > 2:344039/1‑90 (MQ=255)
aCGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGaa < 2:374702/90‑1 (MQ=255)
ggTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAgg < 1:448417/90‑1 (MQ=255)
gcgcTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCata < 1:437252/55‑1 (MQ=255)
gcgcTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCata > 2:437252/1‑55 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 1:489402/1‑90 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 2:177435/1‑90 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 1:152150/1‑90 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 1:275840/1‑90 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 1:20259/1‑90 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 1:186724/1‑90 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 1:155597/1‑90 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGCCATATTCTTAATCCACTGCTGGCAGCAGGTCAGGTACAcggcgg > 2:186506/1‑90 (MQ=255)
cAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCggaat < 2:275840/90‑1 (MQ=255)
aaGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCggaatgg > 1:418201/1‑90 (MQ=255)
|
GAAAGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCACCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGG > NZ_CP009273/2995480‑2995651
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ 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
GCTCTCTGCTGAAAGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCACCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGGGAATGGGCATTGGC > NZ_CP009273/2995470‑2995665
|
GCTCTCTGCTGAAAGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCC > SRR3722114.234925/1‑100 (MQ=60)
tgtgtataagagacagCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCA < SRR3722114.296917/84‑1 (MQ=60)
GCTGAAAGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACC > SRR3722114.27452/1‑100 (MQ=60)
ATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACG < SRR3722114.199556/100‑1 (MQ=60)
ATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACG > SRR3722114.295081/1‑100 (MQ=60)
CACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGCTATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGAT < SRR3722114.406675/100‑1 (MQ=60)
ACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCA > SRR3722114.438488/1‑100 (MQ=60)
ACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATT > SRR3722114.33062/1‑100 (MQ=60)
gctcggagatgtgtataagagacagGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCC < SRR3722114.442640/75‑1 (MQ=60)
TTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCC < SRR3722114.158238/100‑1 (MQ=60)
TGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCA > SRR3722114.510868/1‑100 (MQ=60)
GGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCAC > SRR3722114.98586/1‑100 (MQ=60)
GGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCAC > SRR3722114.379204/1‑100 (MQ=60)
GGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAC < SRR3722114.453985/100‑1 (MQ=60)
ATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGG > SRR3722114.278717/1‑100 (MQ=60)
ATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGG > SRR3722114.20464/1‑100 (MQ=60)
ATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGG > SRR3722114.188558/1‑100 (MQ=60)
ATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGG > SRR3722114.495525/1‑100 (MQ=60)
ATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGG > SRR3722114.157158/1‑100 (MQ=60)
ATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGG > SRR3722114.153689/1‑100 (MQ=60)
GCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGG > SRR3722114.423325/1‑100 (MQ=60)
GTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGGGAATG > SRR3722114.231178/1‑100 (MQ=60)
GTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGGGAATG > SRR3722114.410711/1‑100 (MQ=60)
GTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGGGAATG > SRR3722114.83966/1‑100 (MQ=60)
CGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGGGAATGGGCATTGGC < SRR3722114.461562/100‑1 (MQ=60)
|
GCTCTCTGCTGAAAGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCACCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGGGAATGGGCATTGGC > NZ_CP009273/2995470‑2995665
|
| 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: ‑ |
