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 |
|
A14 F6 I1 R1
|
78 |
2874.5 |
178397650 |
99.0% |
176613673 |
98.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AE015451_phaM1 |
4,741,298 |
C→T |
intergenic (+535/+218) |
gltA CDS (citrate synthase) → / ← yeiW CDS (putative oxidoreductase) |
–/– |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AE015451_phaM1 | 4,741,298 | 0 | C | T | 91.7%
| 28.8
/ ‑3.4
| 12 | intergenic (+535/+218) | gltA CDS (citrate synthase)/yeiW CDS (putative oxidoreductase) | –/– |
| Reads supporting (aligned to +/- strand): ref base C (0/1); new base T (6/5); total (6/6) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.41e-01 |
GGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑AACCTCCGCCAACTGCAATTCGTGAA‑CCAAGCAAAAGGCCCCGAAAAGGCCCTCC‑GCAGCCCCCCCAACCTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCC > AE015451_phaM1/4741179‑4741393
|
ggCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGC‑ATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTcac > 1:186214/1‑149 (MQ=255)
ggCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGC‑ATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTcac < 7:89473/149‑1 (MQ=255)
tGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGC‑ATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGa > 2:337248/1‑149 (MQ=255)
gggTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGC‑ATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTc > 1:216109/1‑134 (MQ=255)
gggTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGC‑ATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTc < 2:216109/134‑1 (MQ=255)
gggTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGC‑ATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGcc < 8:95484/149‑1 (MQ=255)
ataGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGC‑ATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGt > 2:213041/1‑149 (MQ=255)
gTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGC‑ATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACtt > 2:7759/1‑149 (MQ=255)
aGCTCTGGTCACATTCGTGCTTGAGCAGCTTCTGCGACTTGC‑ATTCGTGAATCCAGGC‑ACAGGCCCCGNACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGAc > 1:332954/1‑149 (MQ=255)
gcaTTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGccgt < 5:80238031/97‑3 (MQ=255)
ttCGTGAATCCAGGCAC‑AGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCACCGGCGCCTTGATCACGTTCACACCGCGATAGGTCTTGTa < 6:30094853/99‑1 (MQ=255)
gaCCTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCcgtcctcgtcc < 6:39467151/98‑1 (MQ=255)
|
GGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑AACCTCCGCCAACTGCAATTCGTGAA‑CCAAGCAAAAGGCCCCGAAAAGGCCCTCC‑GCAGCCCCCCCAACCTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTCGTCC > AE015451_phaM1/4741179‑4741393
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
