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 F4 I88 R1
|
217 |
30.5 |
1742422 |
95.9% |
1670982 |
87.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
453,695 |
G→A |
A272T (GCG→ACG) |
clpX → |
ATP‑dependent protease ATP‑binding subunit ClpX |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 453,695 | 0 | G | A | 100.0%
| 138.9
/ NA
| 36 | A272T (GCG→ACG) | clpX | ATP‑dependent protease ATP‑binding subunit ClpX |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (19/17); total (19/17) |
CCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCGCGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCT > NZ_CP009273/453610‑453780
|
ccTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCacgacg > 1:712539/1‑91 (MQ=255)
ccTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCacgacg > 1:648248/1‑91 (MQ=255)
ccTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCacgacg > 1:340373/1‑91 (MQ=255)
cTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACgg > 2:855004/1‑91 (MQ=255)
cTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACgg > 2:766055/1‑91 (MQ=255)
cTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACgg > 2:459242/1‑91 (MQ=255)
gTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTa > 1:53157/1‑91 (MQ=255)
tttGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGc < 2:662826/91‑1 (MQ=255)
tttGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGc < 2:648248/91‑1 (MQ=255)
tgtgGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGa < 1:62350/91‑1 (MQ=255)
tgtgGCGGTGCGTTGGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGa < 2:35132/91‑1 (MQ=255)
tgGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAg < 1:459242/91‑1 (MQ=255)
ggCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGt > 1:195275/1‑91 (MQ=255)
ggCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGt > 1:341528/1‑91 (MQ=255)
ttGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAaagc < 1:244626/91‑1 (MQ=255)
ttGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAaagc < 1:658821/91‑1 (MQ=255)
tGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAaagca > 1:439957/1‑91 (MQ=255)
gTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGa > 1:173497/1‑91 (MQ=255)
gTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGa > 1:480862/1‑91 (MQ=255)
aTTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTgg > 1:420177/1‑91 (MQ=255)
ccACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAg > 1:332787/1‑91 (MQ=255)
ccGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGtt < 1:187686/91‑1 (MQ=255)
gtgtAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGa > 1:4433/1‑91 (MQ=255)
aaaCCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGa < 1:766055/91‑1 (MQ=255)
aaCCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGaa < 1:469996/91‑1 (MQ=255)
aCCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCAAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAg > 1:295576/1‑91 (MQ=255)
cGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGAt > 1:775043/1‑91 (MQ=255)
cGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGAt > 2:597695/1‑91 (MQ=255)
ggCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATc > 2:375675/1‑91 (MQ=255)
gCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCt > 1:100381/1‑91 (MQ=255)
gCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCt > 1:297072/1‑91 (MQ=255)
cGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATc < 2:340373/91‑1 (MQ=255)
cGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATc < 2:313378/91‑1 (MQ=255)
cGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATc < 2:100381/91‑1 (MQ=255)
cGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATc < 1:496583/91‑1 (MQ=255)
ggCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCa < 2:101557/91‑1 (MQ=255)
ttGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGtt < 1:597695/91‑1 (MQ=255)
tGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGttt > 1:789888/1‑91 (MQ=255)
ttGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCt < 2:341528/91‑1 (MQ=255)
|
CCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCGCGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCT > NZ_CP009273/453610‑453780
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ 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
CCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCGCGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCC > NZ_CP009273/453600‑453786
|
CCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACG > SRR3722118.662242/1‑101 (MQ=60)
CCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACG > SRR3722118.728166/1‑101 (MQ=60)
CCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACG > SRR3722118.347410/1‑101 (MQ=60)
CTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTA > SRR3722118.54132/1‑101 (MQ=60)
GTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGT > SRR3722118.199143/1‑101 (MQ=60)
GTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGT > SRR3722118.348585/1‑101 (MQ=60)
TGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAA < SRR3722118.63513/101‑1 (MQ=60)
TGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAG < SRR3722118.468934/101‑1 (MQ=60)
GCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCA > SRR3722118.449223/1‑101 (MQ=60)
GCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGA > SRR3722118.176897/1‑101 (MQ=60)
GCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGA > SRR3722118.491045/1‑101 (MQ=60)
TTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGC < SRR3722118.673078/101‑1 (MQ=60)
TTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGC < SRR3722118.249584/101‑1 (MQ=60)
GGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGG > SRR3722118.429045/1‑101 (MQ=60)
AAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAG > SRR3722118.339645/1‑101 (MQ=60)
ATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGA > SRR3722118.4536/1‑101 (MQ=60)
CCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAG < SRR3722118.191397/101‑1 (MQ=60)
CCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCAAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAG > SRR3722118.301631/1‑101 (MQ=60)
NTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGAT > SRR3722118.671962/1‑101 (MQ=60)
GTGTAGAAGCCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGAT > SRR3722118.792066/1‑101 (MQ=60)
GTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCT > SRR3722118.102231/1‑101 (MQ=60)
GTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCT > SRR3722118.303161/1‑101 (MQ=60)
AAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATC < SRR3722118.782874/101‑1 (MQ=60)
AACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCA < SRR3722118.479913/101‑1 (MQ=60)
GCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTT > SRR3722118.807239/1‑101 (MQ=60)
CGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTC < SRR3722118.507107/101‑1 (MQ=60)
TTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATC < SRR3722118.610417/101‑1 (MQ=60)
GGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCC > SRR3722118.510895/1‑101 (MQ=60)
GGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGAGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCC > SRR3722118.833045/1‑101 (MQ=60)
|
CCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCGCGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCC > NZ_CP009273/453600‑453786
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
