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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
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%
| 114.9
/ NA
| 36 | 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 (19/17); total (19/17) |
CGCTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGTCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCTG > NZ_CP009273/465378‑465549
|
cgcTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGc > 2:32123/1‑90 (MQ=255)
cgcTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGc < 2:1357404/90‑1 (MQ=255)
cgcTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGc < 2:1238220/90‑1 (MQ=255)
ggAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCAt > 2:736175/1‑90 (MQ=255)
ggAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCAt > 2:1452788/1‑90 (MQ=255)
aCGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGc > 2:1201933/1‑81 (MQ=255)
aCGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGc < 1:1201933/81‑1 (MQ=255)
aCGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGc > 1:574139/1‑90 (MQ=255)
gTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGt < 2:834459/90‑1 (MQ=255)
gTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGt < 2:742577/90‑1 (MQ=255)
gTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGt < 1:43926/90‑1 (MQ=255)
gCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGAc > 1:251400/1‑90 (MQ=255)
cTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTc < 2:975049/90‑1 (MQ=255)
aCCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCTGCGTCATTTCGACGTCAGCGa < 1:782941/90‑1 (MQ=255)
ccGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAgg < 2:916791/90‑1 (MQ=255)
ccGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAgg < 2:1184548/90‑1 (MQ=255)
cGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAggg < 1:1092296/90‑1 (MQ=255)
gATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGatat > 2:189614/1‑90 (MQ=255)
tGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTc < 2:22372/90‑1 (MQ=255)
gggTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCtt > 1:312667/1‑90 (MQ=255)
gttATCTGCGGGCCGACTGTTTCCGGCAAAAGTAACCTTTTGCCGCTCATTCAGCGTCATTTCCCCGTCAGCGAGGGGGATATTCGCttt < 1:1082761/88‑1 (MQ=255)
gTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTc > 1:981256/1‑90 (MQ=255)
gTATCTGCGGGCCGACTGGTTCCGGCAAAAGAACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTc > 1:858890/1‑90 (MQ=255)
aTCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCAt > 1:818338/1‑90 (MQ=255)
aTCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCAt < 1:1146291/90‑1 (MQ=255)
gCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGata < 1:1279236/90‑1 (MQ=255)
cGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGatat < 1:607172/90‑1 (MQ=255)
gggCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATAtt > 2:483422/1‑90 (MQ=255)
gggCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATAtt > 1:1199333/1‑90 (MQ=255)
gggCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATAtt > 1:1103123/1‑90 (MQ=255)
gggCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATAtt > 1:636647/1‑90 (MQ=255)
gCCGACTGGTTCCGGCGAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTcc > 2:123848/1‑90 (MQ=255)
gACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCctct > 1:502237/1‑90 (MQ=255)
ggTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACg < 2:1560320/90‑1 (MQ=255)
aaaGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAAc > 1:1549712/1‑90 (MQ=255)
cccTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATa > 2:531882/1‑90 (MQ=255)
gttgcCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCTg > 1:375911/1‑90 (MQ=255)
gttgcCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCTg > 1:594155/1‑90 (MQ=255)
gttgcCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCTg > 2:324386/1‑90 (MQ=255)
gttgcCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCTg > 1:82826/1‑90 (MQ=255)
|
CGCTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGTCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCTG > NZ_CP009273/465378‑465549
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 30 ≤ 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
ACCATCCTGCGCTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGTCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCTGGCGTAG > NZ_CP009273/465369‑465555
|
ACCATCCTGCGCTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCT < SRR3722078.1428200/100‑1 (MQ=60)
CCTGCGCTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTC < SRR3722078.410322/100‑1 (MQ=60)
GCGCTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGC > SRR3722078.580844/1‑100 (MQ=60)
CGCTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCG < SRR3722078.1220782/100‑1 (MQ=60)
CGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGAC > SRR3722078.254471/1‑100 (MQ=60)
GTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACG < SRR3722078.44441/100‑1 (MQ=60)
ACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCTGCGTCATTTCGACGTCAGCGAGGGGGATATT < SRR3722078.793134/100‑1 (MQ=60)
CGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGC < SRR3722078.1108882/100‑1 (MQ=60)
GTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTT > SRR3722078.316495/1‑100 (MQ=60)
CAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTC > SRR3722078.995406/1‑100 (MQ=60)
CAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGAACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTC > SRR3722078.870380/1‑100 (MQ=60)
GATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCAT > SRR3722078.829164/1‑100 (MQ=60)
TGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCctgtctcttatacacatctgacgctgccgacgatggcggcttt > SRR3722078.1402525/1‑57 (MQ=60)
GGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATT > SRR3722078.1119933/1‑100 (MQ=60)
GGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATT > SRR3722078.1218154/1‑100 (MQ=60)
GGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATT > SRR3722078.643962/1‑100 (MQ=60)
GTTATCTGCGGGCCGACTGTTTCCGGCAAAAGTAACCTTTTGCCGCTCATTCAGCGTCATTTCCCCGTCAGCGAGGGGGATATTCGCTTTCATGATATTC < SRR3722078.1099142/100‑1 (MQ=60)
ATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTC < SRR3722078.1163941/100‑1 (MQ=60)
TCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCT > SRR3722078.508181/1‑100 (MQ=60)
GCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGAC < SRR3722078.1299585/100‑1 (MQ=60)
CGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACG < SRR3722078.614187/100‑1 (MQ=60)
GGTTCCGGCAAAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAAC > SRR3722078.1574962/1‑100 (MQ=60)
AAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCTG > SRR3722078.601050/1‑100 (MQ=60)
AAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCTG > SRR3722078.83797/1‑100 (MQ=60)
AAAGTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCTG > SRR3722078.380504/1‑100 (MQ=60)
GTACCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGctgtctcttatacacatctgacg > SRR3722078.418677/1‑77 (MQ=60)
CCCTGTTGCCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTgtctcttatacacatctgacgctgccgacgat > SRR3722078.23934/1‑68 (MQ=60)
|
ACCATCCTGCGCTGGAAAACGTCAATTTCGCCCTGAAACCCGGTCAGATGCTGGGTATCTGCGGGCCGACTGGTTCCGGCAAAAGTACCCTGTTGTCGCTCATTCAGCGTCATTTCGACGTCAGCGAGGGGGATATTCGCTTTCATGATATTCCTCTGACGAAGTTACAACTCGATAGCTGGCGTAG > NZ_CP009273/465369‑465555
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
