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 I231 R1
|
218 |
12.8 |
703680 |
97.2% |
683976 |
86.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
465,464 |
T→C |
S380P (TCG→CCG) |
mdlA → |
SmdA family multidrug ABC transporter permease/ATP‑binding protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 465,464 | 0 | T | C | 100.0%
| 36.7
/ NA
| 12 | S380P (TCG→CCG) | mdlA | SmdA family multidrug ABC transporter permease/ATP‑binding protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (6/6); total (6/6) |
CGCTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGTCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGC > NZ_CP009273/465378‑465547
|
cgcTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGc > 1:280585/1‑90 (MQ=255)
aaaaCGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTc < 1:132477/90‑1 (MQ=255)
aCGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGc > 2:6989/1‑90 (MQ=255)
ccTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGt < 1:124465/90‑1 (MQ=255)
ggTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAgggg < 1:236995/90‑1 (MQ=255)
gTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCAATCAGCGTCATTTCGACGTCAGCGAggggg > 2:339855/1‑90 (MQ=255)
gggTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCtt > 1:72003/1‑90 (MQ=255)
gTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGa < 2:122895/90‑1 (MQ=255)
ggCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCttt > 1:278850/1‑66 (MQ=255)
ggCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCttt < 2:278850/66‑1 (MQ=255)
aCCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGAt > 1:99355/1‑90 (MQ=255)
cTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGc < 2:280585/90‑1 (MQ=255)
|
CGCTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGTCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGC > NZ_CP009273/465378‑465547
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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
GACCATCCTGCGCTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGTCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCTGGCGTAGCCGC > NZ_CP009273/465368‑465559
|
GACCATCCTGCGCTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGC > SRR3722116.284661/1‑100 (MQ=60)
AAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTT < SRR3722116.134031/100‑1 (MQ=60)
CCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGG < SRR3722116.125951/100‑1 (MQ=60)
GGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCT < SRR3722116.240260/100‑1 (MQ=60)
GTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTT > SRR3722116.72909/1‑100 (MQ=60)
GACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTgtctcttataca > SRR3722116.282892/1‑88 (MQ=60)
CGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGAT > SRR3722116.100573/1‑100 (MQ=60)
GTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCTGGCGTAGCCGC > SRR3722116.213953/1‑100 (MQ=60)
|
GACCATCCTGCGCTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGTCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCTGGCGTAGCCGC > NZ_CP009273/465368‑465559
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
