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 I96 R1
|
227 |
23.3 |
882352 |
98.0% |
864704 |
126.9 |
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 | 93.3%
| 41.9
/ ‑3.7
| 16 | A272T (GCG→ACG) | clpX | ATP‑dependent protease ATP‑binding subunit ClpX |
| Reads supporting (aligned to +/- strand): ref base G (1/0); new base A (9/5); total (10/6) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.88e-01 |
CCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCGCGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAAC > NZ_CP009273/453572‑453830
|
ccGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTTGCGGGCTGGGTAAAAGGATTTTCCACCGTGTAGAAAACGGCTCCGGCATTGGGTTTGGCACGCAGGTAAAAACg > 2:398248/1‑138 (MQ=255)
cGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGaa < 1:12164/139‑1 (MQ=255)
aTACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGa < 2:283481/139‑1 (MQ=255)
cTGTTTATTTGTGGCGGTGCGGTTTCCGGACTGGGTTAAGGGGTTTTCCCCCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGGAAAAGCGAAATCCGACAAAGCAAGGGGAGGCGAGGTGCCGGGGCAgg > 1:299947/1‑139 (MQ=255)
tGTTTATTTGTGGCGGTGCGTTTGCCGGGCTGGAGAAAGTGATTTTCCACCGTGTTGAAACCGGCTCCGGCATTGGGTTTTGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGt > 1:424488/1‑139 (MQ=255)
tATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTTCCACCGTGTAGAAAACGGCCCCGGGATTGGGTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGaa > 1:159703/1‑139 (MQ=255)
ccGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGC‑CGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGtt < 1:399950/138‑1 (MQ=255)
tCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGt > 1:291274/1‑139 (MQ=255)
ccGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGgt < 1:339364/139‑1 (MQ=255)
gtgtAGAAACCGGCTCCGGCATTGGTTTTGGCGCGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGgtcg > 2:314926/1‑139 (MQ=255)
aCCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCgg > 1:382140/1‑139 (MQ=255)
aCCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCgg > 1:60355/1‑139 (MQ=255)
gCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGt > 2:346362/1‑139 (MQ=255)
cGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCg < 2:291274/137‑1 (MQ=255)
gCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAAc < 1:309400/139‑1 (MQ=255)
ggCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAAc > 2:417303/1‑139 (MQ=255)
|
CCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCGCGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAAC > NZ_CP009273/453572‑453830
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCGCGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACT > NZ_CP009273/453545‑453831
|
GTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCA < SRR3722119.238123/151‑1 (MQ=60)
CCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAG < SRR3722119.12260/151‑1 (MQ=60)
CCTCTAAGATCCTGTTTATTTGTGGCGGTGCGGTTTCCGGACTGGGTTAAGGGGTTTTCCCCCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGGAAAAGCGAAATCCGACAAAGCAAGGGGAGGCGAGGTGCCGGGGCAGGT > SRR3722119.303021/1‑151 (MQ=60)
CTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGGCTGGAGAAAGTGATTTTCCACCGTGTTGAAACCGGCTCCGGCATTGGGTTTTGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTT > SRR3722119.428738/1‑151 (MQ=60)
AAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTTCCACCGTGTAGAAAACGGCCCCGGGATTGGGTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAAC > SRR3722119.161335/1‑151 (MQ=60)
GCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTC > SRR3722119.294255/1‑151 (MQ=60)
GCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCC < SRR3722119.109667/151‑1 (MQ=60)
GCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGC‑CGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCC < SRR3722119.403944/150‑1 (MQ=60)
CCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCC < SRR3722119.331323/151‑1 (MQ=60)
ACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGT < SRR3722119.342832/151‑1 (MQ=60)
ACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGT > SRR3722119.385979/1‑151 (MQ=60)
ACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGT > SRR3722119.60916/1‑151 (MQ=60)
GGCATTGGTTTTGGCACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAAC < SRR3722119.312555/151‑1 (MQ=60)
GCATTGGTTTTGGTACGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACT > SRR3722119.260658/1‑151 (MQ=60)
|
GTTCCACCGCAAGGTGGGCGTAAACATCCGCAGCAGGAATTCTTGCAGGTTGATACCTCTAAGATCCTGTTTATTTGTGGCGGTGCGTTTGCCGGTCTGGATAAAGTGATTTCCCACCGTGTAGAAACCGGCTCCGGCATTGGTTTTGGCGCGACGGTAAAAGCGAAGTCCGACAAAGCAAGCGAAGGCGAGCTGCTGGCGCAGGTTGAACCGGAAGATCTGATCAAGTTTGGTCTTATCCCTGAGTTTATTGGTCGTCTGCCGGTTGTCGCAACGTTGAATGAACT > NZ_CP009273/453545‑453831
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
