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 |
|
A2 F5 I177 R1
|
141 |
27.5 |
996908 |
97.7% |
973979 |
124.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,036,585 |
A→G |
G171G (GGA→GGG) |
appA → |
bifunctional acid phosphatase/4‑phytase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,036,585 | 0 | A | G | 100.0%
| 46.5
/ NA
| 14 | G171G (GGA→GGG) | appA | bifunctional acid phosphatase/4‑phytase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (10/4); total (10/4) |
GACTGTGCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGAGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCAT > NZ_CP009273/1036457‑1036718
|
gACTGTGCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTg > 2:226027/1‑139 (MQ=255)
tgCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGAc > 1:210883/1‑139 (MQ=255)
gTACATACCCAGGCAGATACGTCCAGTCCAGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAAAGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCggg > 2:385983/1‑138 (MQ=255)
tACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCa < 2:210883/139‑1 (MQ=255)
ggCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACg > 1:50897/1‑139 (MQ=255)
aTTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCt > 2:376143/1‑138 (MQ=255)
tAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGc > 1:281160/1‑138 (MQ=255)
cgcgAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGaaa > 1:187450/1‑139 (MQ=255)
gcgAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAAc < 2:281160/139‑1 (MQ=255)
agcagGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACg < 2:187450/138‑1 (MQ=255)
ggcaggGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACg > 1:66673/1‑133 (MQ=255)
ggcaggGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACg < 2:66673/133‑1 (MQ=255)
ggcaggGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCa > 1:464832/1‑139 (MQ=255)
caggGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCAt > 1:290338/1‑138 (MQ=255)
|
GACTGTGCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGAGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCAT > NZ_CP009273/1036457‑1036718
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GCACCTGACTGTGCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGAGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCATTACCATCGGAACTCAAG > NZ_CP009273/1036451‑1036735
|
GCACCTGACTGTGCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACT > SRR3722131.213353/1‑151 (MQ=60)
GTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGG > SRR3722131.51430/1‑151 (MQ=60)
ATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCA > SRR3722131.284416/1‑150 (MQ=60)
CAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAAC > SRR3722131.189615/1‑151 (MQ=60)
ATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCAT > SRR3722131.469845/1‑151 (MQ=60)
ATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCAT > SRR3722131.67396/1‑151 (MQ=60)
CCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCATT > SRR3722131.293680/1‑150 (MQ=60)
GGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCATTACCtgtctc > SRR3722131.307444/1‑145 (MQ=60)
GGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCATTACCATCGGAACTCAAG < SRR3722131.262182/151‑1 (MQ=60)
|
GCACCTGACTGTGCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGAGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCATTACCATCGGAACTCAAG > NZ_CP009273/1036451‑1036735
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
