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 |
893,176 |
C→T |
44.0% |
V99V (GTG→GTA) |
sapC ← |
predicted antimicrobial peptide transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 893,176 | 0 | C | T | 44.0%
| 5.3
/ 22.5
| 34 | V99V (GTG→GTA) | sapC | predicted antimicrobial peptide transporter subunit |
| Reads supporting (aligned to +/- strand): ref base C (7/12); new base T (5/10); total (12/22) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GAAGGTGCCCAGTACCAGGCCACAGATCGTCGCGGCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGGA > minE/893116‑893243
|
gAAGGTGCCCAGTACCAGGCCACAGATCGTCGCGGCGAGCGTCACCACAAATGCGCCACCTACGGTTgg < 1:1270881/69‑1 (MQ=255)
gAAGGTGCCCAGTACCAGGCCACAGATCGTCGCGGCGAGCGTCACCACAAATGCGCCACCTACGGTTgg < 1:3044971/69‑1 (MQ=255)
gAAGGTGCCCAGTACCAGGCCACAGATCGTCGCGGCGAGCGTCACCACAAATGCGCCACCTACGGTTgg < 1:2873648/69‑1 (MQ=255)
gAAGGTGCCCAGTACCAGGCCACAGATCGTCGCGGCGAGCGTCACCACAAATGCGCCACCTACGGTTgg < 1:2585514/69‑1 (MQ=255)
gAAGGTGCCCAGTACCAGGCCACAGATCGTCGCGGCGAGCGTCACCACAAATGCGCCACCTACGGTTgg < 1:2575829/69‑1 (MQ=255)
gAAGGTGCCCAGTACCAGGCCACAGATCGTCGCGGCGAGCGTCACCACAAATGCGCCACCTACGGTTgg < 1:2394180/69‑1 (MQ=255)
gAAGGTGCCCAGTACCAGGCCACAGATCGTCGCGGCGAGCGTCACCACAAATGCGCCACCTACGGTTgg < 1:1740117/69‑1 (MQ=255)
gAAGGTGCCCAGTACCAGGCCACAGATCGTCGCGGCGAGCGTCACCACAAATGCGCCACCTACGGTTgg < 1:1643909/69‑1 (MQ=255)
gAAGGTGCCCAGTACCAGGCCACAGATCGTCGCGGCGAGCGTCACCACAAATGCGCCACCTACGGTTgg < 1:1623462/69‑1 (MQ=255)
gAAGGTGCCCAGTACCAGGCCACAGATCGTCGCGGCGAGCCTCACCACAAATGCGCCACCTACGGTTgg < 1:55419/69‑1 (MQ=255)
cccAGTACCAGGCCACAGATCGTCGCGGCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCt > 1:1739508/1‑69 (MQ=255)
cccAGTACCAGGCCACAGATCGTCGCGGCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCt > 1:599685/1‑69 (MQ=255)
cccAGTACCAGGCCACAGATCGTCGCGGCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCt > 1:1887895/1‑69 (MQ=255)
cccAGTACCAGGCCACAGATCGTCGCGGCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCt > 1:3131188/1‑69 (MQ=255)
ccAGGCCACAGATCGTCGCGGCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTc > 1:400411/1‑68 (MQ=255)
ccAGGCCACAGATCGTCGCGGCAAGCGTCACCACAAATGCGCCACCCACGGTTCGCGCAGCTCCGCt > 1:2660924/1‑67 (MQ=255)
gcgGCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACa < 1:975907/69‑1 (MQ=255)
gcgGCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACa < 1:33871/69‑1 (MQ=255)
gcgGCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACa < 1:16191/69‑1 (MQ=255)
gcgGCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACa < 1:2071530/69‑1 (MQ=255)
cgGCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACa < 1:806690/68‑1 (MQ=255)
cgGCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACa < 1:703968/68‑1 (MQ=255)
cgGCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACa < 1:56693/68‑1 (MQ=255)
ggCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACa < 1:75497/67‑1 (MQ=255)
ggCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACa < 1:1364191/67‑1 (MQ=255)
aGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGt < 1:1607543/69‑1 (MQ=255)
aGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGt < 1:1763125/69‑1 (MQ=255)
aGCGTCACCACAAATGAGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGt < 1:2770525/69‑1 (MQ=255)
cGTCACCACAAATGCGCCACCTACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGt > 1:213030/1‑67 (MQ=255)
cGTCACCACAAATGCGCCACCTACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGt > 1:1836895/1‑67 (MQ=255)
cGTCACCACAAATGCGCCACCTACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGt > 1:1240798/1‑67 (MQ=255)
cGTCACCACAAATGCGCCACCTACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGt > 1:2757288/1‑67 (MQ=255)
cGTCACCACAAATGCGCCACCTACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGt > 1:1483132/1‑67 (MQ=255)
accacAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAgg > 1:759980/1‑69 (MQ=255)
ccacccacGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTccc < 1:891398/68‑1 (MQ=255)
ccacccacGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTccc < 1:896977/68‑1 (MQ=255)
ccacccacGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTccc < 1:2319915/68‑1 (MQ=255)
cacGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTc > 1:2509081/1‑47 (MQ=255)
cacGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAgg > 1:3015638/1‑67 (MQ=255)
cacGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGga > 1:2226743/1‑68 (MQ=255)
cacGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGga > 1:1862249/1‑68 (MQ=255)
cacGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGga > 1:540297/1‑68 (MQ=255)
cacGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGga > 1:3003721/1‑68 (MQ=255)
cacGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGga > 1:2142238/1‑68 (MQ=255)
cacGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGga > 1:1608712/1‑68 (MQ=255)
|
GAAGGTGCCCAGTACCAGGCCACAGATCGTCGCGGCAAGCGTCACCACAAATGCGCCACCCACGGTTGGCGCAGCTCCGCTCAGTAAACGGCTTAAAACATCGCGTCCGAGGTCGTCAGTCCCCAGGA > minE/893116‑893243
|
| 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
