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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,962,939 |
A→G |
F228S (TTC→TCC) |
cheR ← |
protein‑glutamate O‑methyltransferase CheR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,962,939 | 0 | A | G | 90.9%
| 57.0
/ ‑1.4
| 22 | F228S (TTC→TCC) | cheR | protein‑glutamate O‑methyltransferase CheR |
| Reads supporting (aligned to +/- strand): ref base A (1/1); new base G (9/11); total (10/12) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TCGGGTTTAAGGAGCGGAACAAAGCGGCGCAAAATCTCCTGCTGGGTAGTTTGATCGAAGTAGATCATGACGTTACGACAGAAGATCGCATCAAACGGCCCCGGCACGGTGTACTGTTTCGCCAGTAGATTCAGCGGGGCAAAATCAACATAGTTCGCCAGCT > NZ_CP009273/1962858‑1963020
|
tCGGGTTTAAGGAGCGGAACAAAGCGGCGCAAAATCTCCTGCTGGGTAGTTTGATCGAAGTAGATCATGACGTTACGACAGAAGATCGCa > 1:452896/1‑90 (MQ=255)
cGGAACAAAGCGGCGCAAAATCTCCTGCTGGGTAGTTTGATCGAAGTAGATCATGACGTTACGACAGGAGATCGCATCAAACGGCCCCgg < 2:332699/90‑1 (MQ=255)
gAACAAAGCGGCGCAAAATCTCCTGCTGGGTAGTTTGATCGAAGTAGATCATGACGTTACGACAGGAGATCGCATCAAACGGCCCCGGCa < 1:398469/90‑1 (MQ=255)
aaCAAAGCGGCGCAAAATCTCCTGCTGGGTAGTTTGATCGAAGTAGATCATGACGTTACGACAGGAGATCGCATCAAACGGCCCCGGCAc < 2:451844/90‑1 (MQ=255)
aaCAAAGCGGCGCAAAATCTCCTGCTGGGTAGTTTGATCGAAGTAGATCATGACGTTACGACAGGAGATCGCATCAAACGGCCCCGGCAc < 2:438615/90‑1 (MQ=255)
aaCAAAGCGGCGCAAAATCTCCTGCTGGGTAGTTTGATCGAAGTAGATCATGACGTTACGACAGGAGATCGCATCAAACGGCCCCGGCAc < 2:221017/90‑1 (MQ=255)
gcgcAAAATCTCCTGCTGGGTAGTTTGATCGAAGTAGATCATGACGTTACGACAGGAGATCGCATCAAACGGCCCCGGCAc < 2:508482/81‑1 (MQ=255)
gcgcAAAATCTCCTGCTGGGTAGTTTGATCGAAGTAGATCATGACGTTACGACAGGAGATCGCATCAAACGGCCCCGGCAc > 1:508482/1‑81 (MQ=255)
aaTCTCCTGCTGGGTAGTTTGATCGAAGTAGATCATGACGTTACGACAGGAGATCGCATCAAACGGCCCCGGCACGGTGTACTGTTTCGc < 1:338436/90‑1 (MQ=255)
aGTTTGATCGAAGTAGATCATGACGTTACGACAGGAGATCGCATCAAACGGCCCCgg < 2:645085/57‑1 (MQ=255)
aGTTTGATCGAAGTAGATCATGACGTTACGACAGGAGATCGCATCAAACGGCCCCgg > 1:645085/1‑57 (MQ=255)
tGATCGAAGTAGATCATGACGTTACGACAGGAGATCGCATCAAACGGCCCCGGCACGGTGTACTGTTTCGCCAGTAGATTCAGCGGGGCa < 2:446479/90‑1 (MQ=255)
tGATCGAAGTAGATCATGACGTTACGACAGGAGATCGCATCAAACGGCCCCGGCACGGTGTACTGTTTCGCCAGTAGATTCAGCGGGGCa < 1:334509/90‑1 (MQ=255)
aTCGAAGTAGATCATGACGTTACGACAGGAGATCGCATCAAACGGCCCCGGCAc > 2:274611/1‑54 (MQ=255)
aTCGAAGTAGATCATGACGTTACGACAGGAGATCGCATCAAACGGCCCCGGCAc < 1:274611/54‑1 (MQ=255)
aTCGAAGTAGATCATGACGTTACGACAGGAGATCGCATCAAACGGCCCCGGCACGGTGTACTGTTTCGCCAGTAGATTCAGCGGGGCaaa > 2:297476/1‑90 (MQ=255)
tGACGTTACGACAGGAGATCGCATCAAACGGCCCCGGCACGGTGTACTGTTTCGCCAGTAGATTCAGCGGGGCAAAATCAACATAGTTCg > 2:186119/1‑90 (MQ=255)
aCGTTACGACAGGAGATCGCATCAAACGGCCCCGGCACGGTGTACTGTTTCGCCAGTAGATTCAGCGGGGCAAAATCAACATAGTTCGcc > 2:305441/1‑90 (MQ=255)
aCGTTACGACAGGAGATCGCATCAAACGGCCCCGGCACGGTGTACTGTTTCGCCAGTAGATTCAGCGGGGCAAAATCAACATAGTTCGcc > 1:155434/1‑90 (MQ=255)
cGTTACGACAGAAGATCGCATCAAACGGCCCCGGCACGGTGTACTGTTTCGCCAGTAGATTCAGCGGGGCAAAATCAACATAGTTCGCCa < 2:174482/90‑1 (MQ=255)
ttACGACAGGAGATCGCATCAAACGGCCCCGGCACGGTGTACTGTTTCGCCAGTAGATTCAGCGGGGCAAAATCAACATAGTTCGCCAGc > 1:395438/1‑90 (MQ=255)
tACGACAGGAGATCGCATCAAACGGCCCCGGCACGGTGTACTGTTTCGCCAGTAGATTCAGCGGGGCAAAATCAACATAGTTCGCCAGCt > 2:637434/1‑90 (MQ=255)
|
TCGGGTTTAAGGAGCGGAACAAAGCGGCGCAAAATCTCCTGCTGGGTAGTTTGATCGAAGTAGATCATGACGTTACGACAGAAGATCGCATCAAACGGCCCCGGCACGGTGTACTGTTTCGCCAGTAGATTCAGCGGGGCAAAATCAACATAGTTCGCCAGCT > NZ_CP009273/1962858‑1963020
|
| 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
CCCGCAAACAGCAATCCGTCGGGTTTAAGGAGCGGAACAAAGCGGCGCAAAATCTCCTGCTGGGTAGTTTGATCGAAGTAGATCATGACGTTACGACAGAAGATCGCATCAAACGGCCCCGGCACGGTGTACTGTTTCGCCAGTAGATTCAGCGGGGCAAAATCAACATAGTTCGCCAGCTCCTGACGCACGCGTA > NZ_CP009273/1962840‑1963035
|
CCCGCAAACAGCAATCCGTCGGGTTTAAGGAGCGGAACAAAGCGGCGCAAAATCTCCTGCTGGGTAGTTTGATCGAAGTAGATCATGACGTTACGACAGG > SRR3722112.651361/1‑100 (MQ=60)
CAGCAATCCGTCGGGTTTAAGGAGCGGAACAAAGCGGCGCAAAATCTCCTGCTGGGTAGTTTGATCGAAGTAGATCATGACGTTACGACAGAAGATCGCA > SRR3722112.459258/1‑100 (MQ=60)
GAACAAAGCGGCGCAAAATCTCCTGCTGGGTAGTTTGATCGAAGTAGATCATGACGTTACGACAGGAGATCGCATCAAACGGCCCCGGCACGGTGTACTG < SRR3722112.403710/100‑1 (MQ=60)
GAACAAAGCGGCGCAAAATCTCCTGCTGGGTAGTTTGATCGAAGTAGATCATGACGTTACGACAGGAGATCGCATCAAACGGCCCCGGCACGGTGTACTG > SRR3722112.515896/1‑100 (MQ=60)
cagcgtcagatgtgtataagagacagGGGTAGTTTGATCGAAGTAGATCATGACGTTACGACAGGAGATCGCATCAAACGGCCCCGGCACGGTGTACTGT < SRR3722112.277815/74‑1 (MQ=60)
AATCTCCTGCTGGGTAGTTTGATCGAAGTAGATCATGACGTTACGACAGGAGATCGCATCAAACGGCCCCGGCACGGTGTACTGTTTCGCCAGTAGATTC < SRR3722112.342592/100‑1 (MQ=60)
CCTGCTGGGTAGTTTGATCGAAGTAGATCATGACGTTACGACAGGAGATCGCATCAAACGGCCCCGGCACGGTGTACctgtctcttatacacatctgacg > SRR3722112.655130/1‑77 (MQ=60)
TGATCGAAGTAGATCATGACGTTACGACAGGAGATCGCATCAAACGGCCCCGGCACGGTGTACTGTTTCGCCAGTAGATTCAGCGGGGCAAAATCAACAT < SRR3722112.338573/100‑1 (MQ=60)
GTAGATCATGACGTTACGACAGGAGATCGCATCAAACGGCCCCGGCACGGTGTACTGTTTCGCCAGTAGATTCAGCGGGGCAAAATCAACATAGTTCGCC > SRR3722112.157341/1‑100 (MQ=60)
GATCATGACGTTACGACAGGAGATCGCATCAAACGGCCCCGGCACGGTGTACTGTTTCGCCAGTAGATTCAGCGGGGCAAAATCAACATAGTTCGCCAGC > SRR3722112.400619/1‑100 (MQ=60)
CGTTACGACAGGAGATCGCATCAAACGGCCCCGGCACGGTGTACTGTTTCGCCAGTAGATTCAGCGGGGCAAAATCAACATAGTTCGCCAGCTCCTGACG > SRR3722112.471681/1‑100 (MQ=60)
TACGACAGGAGATCGCATCAAACGGCCCCGGCACGGTGTACTGTTTCGCCAGTAGATTCAGCGGGGCAAAATCAACATAGTTCGCCAGCTCCTGACGCAC > SRR3722112.638808/1‑100 (MQ=60)
CGACAGGAGATCGCATCAAACGGCCCCGGCACGGTGTACTGTTTCGCCAGTAGATTCAGCGGGGCAAAATCAACATAGTTCGCCAGCTCCTGACGCACGC > SRR3722112.220585/1‑100 (MQ=60)
CAGGAGATCGCATCAAACGGCCCCGGCACGGTGTACTGTTTCGCCAGTAGATTCAGCGGGGCAAAATCAACATAGTTCGCCAGCTCCTGACGCACGCGTA > SRR3722112.685050/1‑100 (MQ=60)
|
CCCGCAAACAGCAATCCGTCGGGTTTAAGGAGCGGAACAAAGCGGCGCAAAATCTCCTGCTGGGTAGTTTGATCGAAGTAGATCATGACGTTACGACAGAAGATCGCATCAAACGGCCCCGGCACGGTGTACTGTTTCGCCAGTAGATTCAGCGGGGCAAAATCAACATAGTTCGCCAGCTCCTGACGCACGCGTA > NZ_CP009273/1962840‑1963035
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
