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 I225 R1
|
227 |
21.4 |
1179702 |
97.1% |
1145490 |
86.5 |
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%
| 81.8
/ NA
| 26 | T635A (ACC→GCC) | xdhA | xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (17/9); total (17/9) |
GAAAGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCACCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGG > NZ_CP009273/2995480‑2995651
|
gAAAGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGcc > 1:307043/1‑90 (MQ=255)
gCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCa > 1:355346/1‑90 (MQ=255)
cTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCaa > 1:16143/1‑90 (MQ=255)
cTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCaa > 1:582417/1‑90 (MQ=255)
caccacTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCaa > 1:553919/1‑90 (MQ=255)
ccacTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACg < 2:429822/90‑1 (MQ=255)
aaCCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCAt > 2:305530/1‑90 (MQ=255)
gTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCa > 1:328497/1‑90 (MQ=255)
tttGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCat < 2:326810/90‑1 (MQ=255)
tttGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCat < 1:325814/90‑1 (MQ=255)
ttGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCata < 2:582417/90‑1 (MQ=255)
ttGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCata < 1:305530/90‑1 (MQ=255)
tttGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCa > 1:178939/1‑90 (MQ=255)
ttgttgATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCAc > 2:20431/1‑90 (MQ=255)
ggTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAgg < 2:178939/90‑1 (MQ=255)
gATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAg > 1:546826/1‑90 (MQ=255)
gATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAg > 2:298168/1‑90 (MQ=255)
gcgcTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTacac > 1:254641/1‑90 (MQ=255)
cgcTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcg < 1:574884/90‑1 (MQ=255)
cTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggc < 2:143353/90‑1 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTacac > 2:179662/1‑85 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTacac < 1:179662/85‑1 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 1:87039/1‑90 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 1:389032/1‑90 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 2:498965/1‑90 (MQ=255)
aaGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCggaatgg > 1:246434/1‑90 (MQ=255)
|
GAAAGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCACCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGG > NZ_CP009273/2995480‑2995651
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ 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
GCTCTCTGCTGAAAGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCACCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGGGAATGGGCATTGGCT > NZ_CP009273/2995470‑2995666
|
GCTCTCTGCTGAAAGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCC > SRR3722109.311051/1‑100 (MQ=60)
GCTGCTGAAAGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCA > SRR3722109.360211/1‑100 (MQ=60)
CTGCTGAAAGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAA > SRR3722109.16356/1‑100 (MQ=60)
CTGCTGAAAGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAA > SRR3722109.591232/1‑100 (MQ=60)
CCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAA > SRR3722109.562335/1‑100 (MQ=60)
CTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCctgtctcttatacacatctgacgctgccg > SRR3722109.313454/1‑71 (MQ=60)
ACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCA > SRR3722109.332843/1‑100 (MQ=60)
attgacattcgtcggcagcgtcagatgtgtataagagacagGTGCAAAGTCGCCATGAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATC < SRR3722109.103868/59‑1 (MQ=60)
TTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATC < SRR3722109.330115/100‑1 (MQ=60)
TTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCC < SRR3722109.309511/100‑1 (MQ=60)
TGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCA > SRR3722109.181141/1‑100 (MQ=60)
TCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAG > SRR3722109.555122/1‑100 (MQ=60)
GGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAC > SRR3722109.257681/1‑100 (MQ=60)
ATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGG > SRR3722109.394602/1‑100 (MQ=60)
ATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGG > SRR3722109.88112/1‑100 (MQ=60)
GCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGG > SRR3722109.249327/1‑100 (MQ=60)
GCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGG < SRR3722109.181869/100‑1 (MQ=60)
CGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGGG < SRR3722109.583605/100‑1 (MQ=60)
GTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGGGAATGGGCATTG > SRR3722109.442506/1‑100 (MQ=60)
GCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGGGAATGGGCctgtctc > SRR3722109.236142/1‑93 (MQ=60)
|
GCTCTCTGCTGAAAGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCACCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGGGAATGGGCATTGGCT > NZ_CP009273/2995470‑2995666
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
