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 F25 I1 R1
|
61 |
74.4 |
3161000 |
98.6% |
3116746 |
146.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
4,741,367 |
2 bp→GC |
intergenic (+497/+255) |
gltA → / ← yeiW |
citrate synthase/putative oxidoreductase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 4,741,367 | 0 | C | G | 94.7%
| 59.7
/ ‑2.9
| 19 | intergenic (+497/+256) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| Reads supporting (aligned to +/- strand): ref base C (1/0); new base G (10/8); total (11/8) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.11e-01 |
| * | NC_002947_CJ‑RC | 4,741,368 | 0 | A | C | 94.7%
| 57.9
/ ‑3.2
| 19 | intergenic (+498/+255) | gltA/yeiW | citrate synthase/putative oxidoreductase |
| Reads supporting (aligned to +/- strand): ref base A (1/0); new base C (10/8); total (11/8) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.64e-01 |
GCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGAACCTCCGCCAACTGCAATTCGTGAA‑CCAAGCAAAAGGCCCCGAAAAGGCCCTCC‑GCAGCCCCCCCAACCTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCG > NC_002947_CJ‑RC/4741232‑4741497
||
gCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCgga > 6:78216/1‑147 (MQ=255)
gTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGtcctcctgcag > 5:210028/1‑144 (MQ=255)
tAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGc > 3:246877/1‑149 (MQ=255)
tAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGc > 7:138065/1‑149 (MQ=255)
cagcaCGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGcgcctcga < 1:438/149‑5 (MQ=255)
tCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAg > 6:277929/1‑149 (MQ=255)
gTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCtt < 8:138065/149‑1 (MQ=255)
tataGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTg < 6:210028/149‑1 (MQ=255)
gTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACtt > 6:222340/1‑149 (MQ=255)
gTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACtt < 7:5580/149‑1 (MQ=255)
gTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGACCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCTCGATAGGCCTTGTACTTGGACCCGGCCa > 6:281393/1‑149 (MQ=255)
tCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCAc > 8:325087/1‑149 (MQ=255)
cACCTTCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGAATCCAGGCACAA‑GCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCAcc > 3:94226/1‑149 (MQ=255)
ttCGTGCTTGAGCAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCAc > 8:209887/1‑149 (MQ=255)
acttgcaTTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCcgtcc < 7:199384/143‑1 (MQ=255)
cttgcaTTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCcgtcct < 6:376830/144‑1 (MQ=255)
tgcaTTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCcgtcctcg > 5:286562/4‑149 (MQ=255)
gcaTTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCcgtcctc < 1:15880/145‑1 (MQ=255)
gcaTTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCcgtcctc < 4:246877/145‑1 (MQ=255)
||
GCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGAACCTCCGCCAACTGCAATTCGTGAA‑CCAAGCAAAAGGCCCCGAAAAGGCCCTCC‑GCAGCCCCCCCAACCTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCG > NC_002947_CJ‑RC/4741232‑4741497
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
