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 |
|
A35 F30 I1 R1
|
29 |
21.9 |
747794 |
99.4% |
743307 |
139.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,337,667 |
C→A |
A75A (GCG→GCT) |
mlaC ← |
intermembrane phospholipid transport system ‑ periplasmic binding protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,337,667 | 0 | C | A | 91.7%
| 33.0
/ ‑2.0
| 12 | A75A (GCG→GCT) | mlaC | intermembrane phospholipid transport system ‑ periplasmic binding protein |
| Reads supporting (aligned to +/- strand): ref base C (1/0); new base A (3/8); total (4/8) |
| Fisher's exact test for biased strand distribution p-value = 3.33e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01 |
ATCGCCAGCGCCTGACCGTAAGCCTGCTTCAGGTACTCACGGAAAGCGGCAAAGTAGGCTTCACGTTGAGCAGGGGTCGCACTCTTGTAATACTGGCCCAGCACCAGCGCACCGGCGTATTTCACCTGTACGTATGGCAGCAGTTCCTGATCAACAATGGTACGCAGATAATCCGGGTTGGCCCGAATTTGCGGTTGCTCATTCTTCAGGCGATCGAACGTTTTCTGCGCCGCCTCGTCCATC > NC_000913/3337560‑3337802
|
aTCGCCAGCGCCTGACCGTAAGCCTGCTTCAGGTACTCACGGAAAGCGGCAAAGTAGGCTTCACGTTGAGCAGGGGTCGCACTCTTGTAATACTGGCCCAGCACCAGAGCACCGGCGTATTTCACCTGTACGTATGgcag < 1:167418/140‑1 (MQ=255)
aTCGCCAGCGCCTGACCGTAAGCCTGCTTCAGGTACTCACGGAAAGCGGCAAAGTAGGCTTCACGTTGAGCAGGGGTCGCACTCTTGTAATACTGGCCCAGCACCAGAGCACCGGCGTATTTCACCTGTACGTATGgcag < 2:304313/140‑1 (MQ=255)
gACCGTAAGCCTGCTTCAGGTACTCACGGAAAGCGGCAAAGTAGGCTTCACGTTGAGCAGGGGTCGCACTCTTGTAATACTGGCCCAGCACCAGAGCACCGGCGTATTTCACCTGTACGTATGGCAGCAGTTCCTGATca > 2:30907/1‑140 (MQ=255)
aCCGTAAGCCTGCTTCAGGTACTCACGGAAAGCGGCAAAGTAGGCTTCACGTTGAGCAGGGGTCGCACTCTTGTAATACTGGCCCAGCACCAGAGCACCGGCGTATTTCACCTGTACGTATGGCAGCAGTTCCTGATcaa < 2:217322/140‑1 (MQ=255)
tAAGCCTGCTTCAGGTACTCACGGAAAGCGGCAAAGTAGGCTTCACGTTGAGCAGGGGTCGCACTCTTGTAATACTGGCCCAGCACCAGAGCACCGGCGTATTTCACCTGTACGTATGGCAGCAGTTCCTGATCAACAAt < 1:110297/140‑1 (MQ=255)
gTAGGCTTCACGTTGAGCAGGGGTCGCACTCTTGTAATACTGGCCCAGCACCAGAGCACCGGCGTATTTCACCTGTACGTATGGCAGCAGTTCCTGATCAACAATGGTACGCAGATAATCCGGGTTGGCCCGAATTTGCg < 1:55183/140‑1 (MQ=255)
ttGAGCAGGGGTCGCACTCTTGTAATACTGGCCCAGCACCAGAGCACCGGCGTATTTCACCTGTACGTATGGCAGCAGTTCCTGATCAACAATGGTACGCAGATAATCCGGGTTGGCCCGAATTTGCGGTTGCTCAttct < 2:12573/140‑1 (MQ=255)
tGGCCCAGCACCAGCGCACCGGCGTATTTCACCTGTACGTATGGCAGCAGTTCCTGATCAACAATGGTACGCAGATAATCCGGGTTGGCCCGAATTTGCGGTTGCTCATTCTTCAGGCGATCGAACGTTTTCTGcgccgc > 1:131374/1‑140 (MQ=255)
ggCCCAGCACCAGAGCACCGGCGTATTTCACCTGTACGTATGGCAGCAGTTCCTGATCAACAATGGTACGCAGATAATCCGGGTTGGCCCGAATTTGCGGTTGCTCATTCTTCAGGCGATCGAACGTTTTCTGCgccgcc > 2:333337/1‑140 (MQ=255)
cccAGCACCAGAGCACCGGCGTATTTCACCTGTACGTATGGCAGCAGTTCCTGATCAACAATGGTACGCAGATAATCCGGGTTGGCCCGAATTTGCGGTTGCTCATTCTTCAGGCGATCGAACGTTTTCTGCGCCGCCTc > 2:66218/1‑140 (MQ=255)
cACCAGAGCACCGGCGTATTTCACCTGTACGTATGGCAGCAGTTCCTGATCAACAATGGTACGCAGATAATCCGGGTTGGCCCGAATTTGCGGTTGCTCATTCTTCAGGCGATCGAACGTTTTCTGCGCCGCCTCGTCCa < 2:232471/140‑1 (MQ=255)
ccAGAGCACCGGCGTATTTCACCTGTACGTATGGCAGCAGTTCCTGATCAACAATGGTACGCAGATAATCCGGGTTGGCCCGAATTTGCGGTTGCTCATTCTTCAGGCGATCGAACGTTTTCTGCGCCGCCTCGTCCATc < 2:198012/140‑1 (MQ=255)
|
ATCGCCAGCGCCTGACCGTAAGCCTGCTTCAGGTACTCACGGAAAGCGGCAAAGTAGGCTTCACGTTGAGCAGGGGTCGCACTCTTGTAATACTGGCCCAGCACCAGCGCACCGGCGTATTTCACCTGTACGTATGGCAGCAGTTCCTGATCAACAATGGTACGCAGATAATCCGGGTTGGCCCGAATTTGCGGTTGCTCATTCTTCAGGCGATCGAACGTTTTCTGCGCCGCCTCGTCCATC > NC_000913/3337560‑3337802
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
