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 I229 R1
|
214 |
17.4 |
943020 |
97.5% |
919444 |
87.1 |
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%
| 80.6
/ NA
| 27 | T635A (ACC→GCC) | xdhA | xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (13/14); total (13/14) |
ATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCACCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAAT > NZ_CP009273/2995489‑2995649
|
aTCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGc < 1:373020/90‑1 (MQ=255)
cAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCAt < 1:271085/90‑1 (MQ=255)
aaaaCCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATACTGCGCTGTGCAAAGTCGCCATCAACCGCATc > 1:198376/1‑90 (MQ=255)
aaCCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATACTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCAt < 2:198376/90‑1 (MQ=255)
aCCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTc > 2:354166/1‑90 (MQ=255)
aCCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTc > 2:279145/1‑90 (MQ=255)
ccGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCa > 1:337362/1‑90 (MQ=255)
ccGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCa < 1:102463/90‑1 (MQ=255)
cGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAg < 1:170304/90‑1 (MQ=255)
tttGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCat < 1:354166/90‑1 (MQ=255)
ttGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCata < 1:379931/90‑1 (MQ=255)
gTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTa > 1:53036/1‑90 (MQ=255)
gTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTa > 2:381315/1‑90 (MQ=255)
gTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTa > 1:409512/1‑90 (MQ=255)
gACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGa > 1:435608/1‑90 (MQ=255)
tCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTc < 1:62764/90‑1 (MQ=255)
ttGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTac < 2:71247/90‑1 (MQ=255)
gcgcTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTacac < 1:349451/90‑1 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 2:186484/1‑90 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 1:239213/1‑90 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg < 2:360930/90‑1 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 2:372832/1‑90 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 2:428736/1‑90 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 2:45668/1‑90 (MQ=255)
cAATGTCGCCAGCAACCGCATCCCCAACGTTCATGATTCAGAGCATATTCTTAACCCCCTGCTGGCAGAAGGTCAGGTAGACGGCggaat < 2:50556/90‑1 (MQ=255)
cAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCggaat < 1:217154/90‑1 (MQ=255)
cAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCggaat < 2:409512/90‑1 (MQ=255)
|
ATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCACCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAAT > NZ_CP009273/2995489‑2995649
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 32 ≤ 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
CTCTGCTGAAAGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCACCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGGGAATGGGCAT > NZ_CP009273/2995473‑2995661
|
CTCTGCTGAAAGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATC < SRR3722113.174454/100‑1 (MQ=60)
AAGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATACTGCGCTGTGCAAAGTCGCCATCAACCGCATC > SRR3722113.199915/1‑100 (MQ=60)
ATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACG < SRR3722113.376892/100‑1 (MQ=60)
CAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTT < SRR3722113.273477/100‑1 (MQ=60)
CACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCA > SRR3722113.340792/1‑100 (MQ=60)
CCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTC < SRR3722113.103381/100‑1 (MQ=60)
CGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCT < SRR3722113.171678/100‑1 (MQ=60)
GCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTA > SRR3722113.53485/1‑100 (MQ=60)
GCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTA > SRR3722113.413823/1‑100 (MQ=60)
TTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATC < SRR3722113.357776/100‑1 (MQ=60)
TTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCC < SRR3722113.383892/100‑1 (MQ=60)
TTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGA > SRR3722113.440219/1‑100 (MQ=60)
TCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTGCACGG < SRR3722113.63321/100‑1 (MQ=60)
ATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGG > SRR3722113.241258/1‑100 (MQ=60)
gacagGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGG < SRR3722113.390566/95‑1 (MQ=60)
GCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGG < SRR3722113.353008/100‑1 (MQ=60)
GTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGGGAATG > SRR3722113.196407/1‑100 (MQ=60)
GTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGGGAATG > SRR3722113.184338/1‑100 (MQ=60)
GTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGAGGAATGGGAATG > SRR3722113.132770/1‑100 (MQ=60)
CAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGGGAATGGGC < SRR3722113.218877/100‑1 (MQ=60)
AAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGGGAATGGGCAT > SRR3722113.223899/1‑100 (MQ=60)
|
CTCTGCTGAAAGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCACCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGGGAATGGGCAT > NZ_CP009273/2995473‑2995661
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
