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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
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%
| 45.4
/ NA
| 15 | 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 (7/8); total (7/8) |
CGCTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGTCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTAC > NZ_CP009273/465378‑465536
|
cgcTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGc > 2:384743/1‑90 (MQ=255)
aaaaCATCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTc < 2:54087/90‑1 (MQ=255)
aCGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGc > 1:108598/1‑90 (MQ=255)
aaTTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCAt > 2:88456/1‑90 (MQ=255)
gCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGAc < 2:179591/90‑1 (MQ=255)
cGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAggg > 1:187439/1‑90 (MQ=255)
ggTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCttt < 1:107661/90‑1 (MQ=255)
aTCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCAt > 1:517599/1‑90 (MQ=255)
aTCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCAt < 2:517599/90‑1 (MQ=255)
cTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTc < 1:38698/86‑1 (MQ=255)
cTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTc > 2:38698/1‑86 (MQ=255)
cGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGatat < 1:455171/90‑1 (MQ=255)
gCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTcc > 1:360804/1‑90 (MQ=255)
cGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGtt < 2:187439/90‑1 (MQ=255)
gCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTAc < 2:274677/90‑1 (MQ=255)
|
CGCTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGTCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTAC > NZ_CP009273/465378‑465536
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ 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
GCGCTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGTCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCTGGCGTAGCCGCCTGG > NZ_CP009273/465377‑465563
|
GCGCTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGC > SRR3722111.109962/1‑100 (MQ=60)
CCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGG > SRR3722111.189777/1‑100 (MQ=60)
GATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCAT > SRR3722111.525676/1‑100 (MQ=60)
GGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTC < SRR3722111.109013/100‑1 (MQ=60)
GTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCC > SRR3722111.365808/1‑100 (MQ=60)
GTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCC < SRR3722111.39158/100‑1 (MQ=60)
CGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACG < SRR3722111.462076/100‑1 (MQ=60)
CCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCTGGCGTAG > SRR3722111.151114/1‑100 (MQ=60)
CCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCtgtctcttatacacatctgacgctgccgacgaatgtcaatgtgtagatctcggtggt > SRR3722111.243268/1‑43 (MQ=60)
|
GCGCTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGTCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCTGGCGTAGCCGCCTGG > NZ_CP009273/465377‑465563
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
