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 |
|
A5 F91 I0 R1
|
918 |
53.4 |
2573728 |
94.2% |
2424451 |
136.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_002947 |
4,741,285 |
2 bp→CT |
100% |
intergenic (+476/+275) |
gltA → / ← yeiW |
citrate synthase/putative oxidoreductase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947 | 4,741,285 | 0 | A | C | 95.7%
| 67.0
/ ‑4.6
| 23 | intergenic (+476/+276) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base C (12/10); total (12/11) |
| Fisher's exact test for biased strand distribution p-value = 4.78e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.39e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| * | NC_002947 | 4,741,286 | 0 | C | T | 96.4%
| 65.5
/ ‑5.9
| 23 | intergenic (+477/+275) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| Reads supporting (aligned to +/- strand): ref base C (0/1); new base T (12/10); total (12/11) |
| Fisher's exact test for biased strand distribution p-value = 4.78e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑AA‑CCT‑CC‑GCCAAC‑TGCATTCGTGAA‑CCAAGCAACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGC > NC_002947/4741175‑4741401
||
ctTGATGGTCGTGATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CA‑GCT‑TC‑CCCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGtc < 1:105409/150‑1 (MQ=255)
gATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGtcctc > 1:1156116/1‑150 (MQ=255)
aTGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGtcctcc < 2:1156116/150‑1 (MQ=255)
tGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGATCTAATCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGAAGTAGTGAG‑TCCAGGCACAGGCCCCGGACACGTcctcct > 1:286802/1‑150 (MQ=255)
tCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CA‑GCT‑TCTGCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCa > 2:897385/1‑150 (MQ=255)
aCGGAATCACGCGGCGTCACCGGCCATGGCGGATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CA‑GCT‑TCTGCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGCACACGTCCTCCTGCAGCGCCTCGACCTTg > 1:647212/1‑150 (MQ=255)
aaTCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCa > 2:241265/1‑150 (MQ=255)
aCCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATc > 1:31289/1‑150 (MQ=255)
cGGCCATGGCGTATTGAACTGGGTATAGGTACAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTT‑CT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCAc < 2:668603/150‑1 (MQ=255)
gCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CA‑GCT‑TCTGCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGGCACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACgg > 1:589126/1‑150 (MQ=255)
tATTGAACTGGGTATAGGTCCAGCTCTAGTCACATTCGTATGTGAG‑CA‑GCTGCT‑GCGTCT‑TGCATTCGTGGA‑TCCAGGCCGGGGGCGTATTTACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATAACGGTCACACcgc > 1:931617/1‑150 (MQ=255)
aaCTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAg < 2:931617/150‑1 (MQ=255)
aaCTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAg > 2:678514/1‑150 (MQ=255)
ggTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCtt < 2:31289/150‑1 (MQ=255)
ggTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCtt < 2:647212/150‑1 (MQ=255)
gtcgctgCTCTGGTCCCCTTCGTGCTTGCGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACtt < 2:589126/144‑1 (MQ=255)
ggTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACtt < 2:1274852/150‑1 (MQ=255)
gTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTg > 1:1228349/1‑150 (MQ=255)
ctGGTCACCTTCGTGCTTGAG‑CA‑GCT‑TCTGCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGc < 1:1191572/150‑1 (MQ=255)
tGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACg > 1:648445/1‑114 (MQ=255)
tGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACg < 2:648445/114‑1 (MQ=255)
tCACCTTCGTGCTTGAG‑CA‑GCT‑TCTGCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGa > 1:449355/1‑85 (MQ=255)
tCACCTTCGTGCTTGAG‑CA‑GCT‑TCTGCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGa < 2:449355/85‑1 (MQ=255)
||
CTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑AA‑CCT‑CC‑GCCAAC‑TGCATTCGTGAA‑CCAAGCAACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGC > NC_002947/4741175‑4741401
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
