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 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,600,816 |
2 bp→AT |
100% |
coding (1086‑1087/1425 nt) |
murP → |
fused predicted enzyme IIBC components of PTS |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,600,816 | 0 | G | A | 85.9%
| 18.8
/ ‑2.7
| 14 | A362A (GCG→GCA) | murP | fused predicted enzyme IIBC components of PTS |
| Reads supporting (aligned to +/- strand): ref base G (0/2); new base A (5/7); total (5/9) |
| Fisher's exact test for biased strand distribution p-value = 5.05e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.76e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| * | minE | 1,600,817 | 0 | C | T | 85.9%
| 18.8
/ ‑2.8
| 14 | L363L (CTA→TTA) | murP | fused predicted enzyme IIBC components of PTS |
| Reads supporting (aligned to +/- strand): ref base C (0/2); new base T (5/7); total (5/9) |
| Fisher's exact test for biased strand distribution p-value = 5.05e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.76e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
AGGCGCGGGCCAGGTGGGCGCGGCGCTGGCACTCTACTGGCGGGCGCAACCGCACAGTGCGCTACGCAGTCAGGTACGCGGGGCGATTATTCCCGGCCTGCTGGGCGTTGGTGAACCGCTGATTTAC > minE/1600756‑1600882
||
aGGCGCGGGCCAGGTGGGCGCGGCGCTGGCACTCTACTGGCGGGCGCAACCGCACAGTGCGCTACGCa < 1:2012981/68‑1 (MQ=255)
aaCCGCACAGTGCATTACGCAGTCAGGTCCGCGGGGCGATTATTcc < 1:2132299/46‑1 (MQ=255)
aaCCGCACAGTGCATTACGCAGTCAGGTCCGCGGGGCGATTATTcc < 1:2384637/46‑1 (MQ=255)
aaCCGCACAGTGCATTACGCAGTCAGGTCCGCGGGGCGATTATTcc < 1:2966939/46‑1 (MQ=255)
aaCCGCACAGTGCATTACGCAGTCAGGTCCGCGGGGCGATTATTcc < 1:298809/46‑1 (MQ=255)
aaCCGCACAGTGCATTACGCAGTCAGGTCCGCGGGGCGATTATTcc < 1:628919/46‑1 (MQ=255)
aaCCGCACAGTGCATTACGCAGTCAGGTCCGCGGGGCGATTATTcc < 1:906550/46‑1 (MQ=255)
aaCCGCACAGTGCATTACGCAGTCAGGTCCGCGGGGCGATTATTcc < 1:919597/46‑1 (MQ=255)
ccGCACAGTGCATTACGCAGTCAGGTCCGCGGGGCGATTATTCCCGGTCTGCTTGGCGTTGGCGAAcc > 1:2996069/1‑68 (MQ=255)
ccGCACAGTGCATTACGCAGTCAGGTCCGCGGGGCGATTATTCCCGGTCTGCTTGGCGTTGGCGAACCg > 1:2625751/1‑69 (MQ=255)
ccGCACAGTGCATTACGCAGTCAGGTCCGCGGGGCGATTATTCCCGGTCTGCTTGGCGTTGGCGAACCg > 1:3322573/1‑69 (MQ=255)
ccGCACAGTGCATTACGCAGTCAGGTCCGCGGGGCGATTATTCCCGGTCTGCTTGGCGTTGGCGAACCg > 1:382316/1‑69 (MQ=255)
ccGCACAGTGCATTACGCAGTCAGGTCCGCGGGGCGATTATTCCCGGTCTGCTTGGCGTTGGCGAACCg > 1:489666/1‑69 (MQ=255)
acaGTGCGCTACGCAGTCAGGTACGCGGGGCGATTATTCCCGGCCTGCTGGGCGTTGGTGAACCGCTGa < 1:2061341/69‑1 (MQ=255)
gcgcTACGCAGTCAGGTACGCGGGGCGATTATTCCCGGCCTGCTGGGCGTTGGTGAACCGCTGATTTAc > 1:947300/1‑69 (MQ=255)
||
AGGCGCGGGCCAGGTGGGCGCGGCGCTGGCACTCTACTGGCGGGCGCAACCGCACAGTGCGCTACGCAGTCAGGTACGCGGGGCGATTATTCCCGGCCTGCTGGGCGTTGGTGAACCGCTGATTTAC > minE/1600756‑1600882
|
| 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
