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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
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 | 82.2%
| 93.4
/ 14.3
| 45 | T635A (ACC→GCC) | xdhA | xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| Reads supporting (aligned to +/- strand): ref base A (3/5); new base G (22/15); total (25/20) |
| Fisher's exact test for biased strand distribution p-value = 4.35e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GAAAGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCACCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAAT > NZ_CP009273/2995480‑2995649
|
gAAAGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGcc > 1:742413/1‑90 (MQ=255)
aGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATc < 1:363753/90‑1 (MQ=255)
ccATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAAcc > 1:494464/1‑90 (MQ=255)
aTCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCACCATCAACCGc < 2:690591/90‑1 (MQ=255)
caccacTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCaa < 2:446292/90‑1 (MQ=255)
caccacTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCaa < 2:742413/90‑1 (MQ=255)
aaCCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCAt < 2:594651/90‑1 (MQ=255)
aCCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTc > 2:702071/1‑90 (MQ=255)
aCCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCACCATCAACCGCATCCTCAACGTTCATGATTc > 1:115218/1‑90 (MQ=255)
ccGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCa > 1:323715/1‑90 (MQ=255)
ccGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCa < 1:96715/90‑1 (MQ=255)
tttGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCat < 1:202697/90‑1 (MQ=255)
tttGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCat < 2:58596/90‑1 (MQ=255)
ttGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCata < 1:156717/90‑1 (MQ=255)
gTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTa > 2:71592/1‑90 (MQ=255)
tttGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCAt < 1:170977/66‑1 (MQ=255)
tttGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCAt > 2:170977/1‑66 (MQ=255)
ttgttgATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCAc > 2:51857/1‑90 (MQ=255)
tCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGc > 2:570255/1‑90 (MQ=255)
cTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCa < 2:831576/90‑1 (MQ=255)
aCGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGaa < 1:51857/90‑1 (MQ=255)
aCGGTCGATATTGCGCTGTGCAAAGTCACCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGaa < 2:615715/90‑1 (MQ=255)
cGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCa > 1:820517/1‑90 (MQ=255)
atatTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAgg < 1:648162/90‑1 (MQ=255)
gcgcTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTacac > 1:773199/1‑90 (MQ=255)
cTGTGCAAAGTCACCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggc < 2:279257/90‑1 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCtt < 1:797704/55‑1 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCtt > 2:797704/1‑55 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 1:90549/1‑90 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 1:327208/1‑90 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 1:585238/1‑90 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 2:59693/1‑90 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 1:706051/1‑90 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 1:709559/1‑90 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 2:242581/1‑90 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 1:792741/1‑90 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 2:168568/1‑90 (MQ=255)
gtgCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 2:121113/1‑90 (MQ=255)
gtgCAAAGTCACCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 2:63326/1‑90 (MQ=255)
gtgCAAAGTCACCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAcggcgg > 2:146441/1‑90 (MQ=255)
cAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCggaat < 1:12330/90‑1 (MQ=255)
cAAAGTCACCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCggaat < 2:398726/90‑1 (MQ=255)
cAAAGTCACCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCggaat < 1:63326/90‑1 (MQ=255)
aaGTCGCCATCAACCGCATCCTCAACGTTCATGATTCa < 2:226851/38‑1 (MQ=38)
aaGTCGCCATCAACCGCATCCTCAACGTTCATGATTCa > 1:226851/1‑38 (MQ=38)
|
GAAAGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCACCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAAT > NZ_CP009273/2995480‑2995649
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ 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 > SRR3722079.750353/1‑100 (MQ=60)
GCTGAAAGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACC > SRR3722079.498851/1‑100 (MQ=60)
AGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCC < SRR3722079.366603/100‑1 (MQ=60)
CCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCACCATCAACCGCATCCTCAACGTTCATGATTC > SRR3722079.116163/1‑100 (MQ=60)
CACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCA > SRR3722079.326314/1‑100 (MQ=60)
tgtataagagacagTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGC < SRR3722079.172465/86‑1 (MQ=60)
CCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTC < SRR3722079.97477/100‑1 (MQ=60)
TTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATC < SRR3722079.204446/100‑1 (MQ=60)
TTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCC < SRR3722079.158074/100‑1 (MQ=60)
gctcggagatgtgtataagagacaGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGC < SRR3722079.806251/76‑1 (MQ=60)
ATCTGACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCA > SRR3722079.829305/1‑100 (MQ=60)
ACGGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTAC < SRR3722079.52266/100‑1 (MQ=60)
GGTCGATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACAC > SRR3722079.781483/1‑100 (MQ=60)
ATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGG > SRR3722079.591045/1‑100 (MQ=60)
ATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGG > SRR3722079.91264/1‑100 (MQ=60)
ATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGG < SRR3722079.654860/100‑1 (MQ=60)
ATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGG > SRR3722079.713541/1‑100 (MQ=60)
ATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGG > SRR3722079.717093/1‑100 (MQ=60)
ATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGG > SRR3722079.329828/1‑100 (MQ=60)
ATATTGCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGG > SRR3722079.801240/1‑100 (MQ=60)
GCGCTGTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCctgtctcttatacacatctccgagcccacgagaccagagagg > SRR3722079.228778/1‑58 (MQ=60)
GTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACtgtctcttatacacatc > SRR3722079.841902/1‑83 (MQ=60)
GTGCAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGGGAATG > SRR3722079.442311/1‑100 (MQ=60)
CAAAGTCGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGGGAATGGGC < SRR3722079.12418/100‑1 (MQ=60)
CAAAGTCACCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGGGAATGGGC < SRR3722079.63843/100‑1 (MQ=60)
CGCCATCAACCGCATCCTCAACGTTGATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGGGAATGGGCATTGGC < SRR3722079.629029/100‑1 (MQ=60)
CGCCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGGGAATGGGCATTGGC < SRR3722079.72190/100‑1 (MQ=60)
|
GCTCTCTGCTGAAAGCTCCATCAAAACCACCACTAACCCACCGGCGTTTGGCTGTACCTTTGTTGATCTGACGGTCGATATTGCGCTGTGCAAAGTCACCATCAACCGCATCCTCAACGTTCATGATTCAGGGCATATTCTTAATCCACTGCTGGCAGAAGGTCAGGTACACGGCGGAATGGGAATGGGCATTGGC > NZ_CP009273/2995470‑2995665
|
| 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: ‑ |
