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 I211 R1
|
223 |
18.0 |
1007644 |
96.3% |
970361 |
85.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,579,168 |
T→C |
E339G (GAA→GGA) |
ggt ← |
gamma‑glutamyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,579,168 | 0 | T | C | 100.0%
| 46.0
/ NA
| 15 | E339G (GAA→GGA) | ggt | gamma‑glutamyltransferase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (8/7); total (8/7) |
ATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTCAT > NZ_CP009273/3579089‑3579250
|
aTCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTc < 2:502674/90‑1 (MQ=255)
tttGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCggcgtaggcgta > 1:85898/1‑90 (MQ=255)
aGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCg > 1:268563/1‑90 (MQ=255)
aGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCg > 1:489585/1‑90 (MQ=255)
tttATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTc < 1:376789/90‑1 (MQ=255)
tGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCa < 2:280400/90‑1 (MQ=255)
tGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCa < 2:61678/90‑1 (MQ=255)
gTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATg > 2:499298/1‑90 (MQ=255)
gcgcCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGAttt > 1:394707/1‑90 (MQ=255)
gcCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTgc < 2:268563/90‑1 (MQ=255)
aCGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTgcatcgcat < 2:264900/90‑1 (MQ=255)
aaaaTCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCaaa < 2:117161/90‑1 (MQ=255)
aaaaTCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCaaa > 2:297040/1‑90 (MQ=255)
aaTCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGc > 2:446837/1‑90 (MQ=255)
aaGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTCat > 2:491619/1‑90 (MQ=255)
|
ATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTCAT > NZ_CP009273/3579089‑3579250
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TTATTGATATCAATTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTCATATCGAAGTTTTCCA > NZ_CP009273/3579072‑3579264
|
TTATTGATATCAATTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCG < SRR3722094.491086/100‑1 (MQ=60)
CGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTA > SRR3722094.87131/1‑100 (MQ=60)
GATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCG > SRR3722094.272569/1‑100 (MQ=60)
GATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCG > SRR3722094.498218/1‑100 (MQ=60)
TTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATT < SRR3722094.383186/100‑1 (MQ=60)
TTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTT > SRR3722094.401498/1‑100 (MQ=60)
AAGATATCCCGAGCGGTCGGCGTAGGCGGATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTCATATCGAAGTTT > SRR3722094.74730/1‑100 (MQ=60)
TATCCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTCATATCGAAGTTTTCCA > SRR3722094.441769/1‑100 (MQ=60)
|
TTATTGATATCAATTTGATCGGCAATAGATTTGGCATAGGCTTTATTGGTCAGCGCCTGCCACGGTACTTTGACAAAATCCGGGTCGCCAAGATATTCCGAGCGGTCGGCGTAGGCGTATTTCTCCGCTTCTGCCATGATTTGCATCGCATCGGCGCTGCCAAAGCCGTATTTCTTCATATCGAAGTTTTCCA > NZ_CP009273/3579072‑3579264
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
