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 |
1,892,400 |
A→G |
100% |
D160D (GAT→GAC) |
ygdL ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,892,400 | 0 | A | G | 79.2%
| 58.9
/ 8.2
| 43 | D160D (GAT→GAC) | ygdL | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (5/4); new base G (34/0); total (39/4) |
| Fisher's exact test for biased strand distribution p-value = 1.02e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.35e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CGCCAGCGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGATCAATCTGCCCACCCGCGCCACCGGTTGTGACCAGTGGGATTTTATTGCGCCGACAATAAGCAATC > minE/1892346‑1892466
|
cgccAGCGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGATCAATCTGCCCAcc < 1:700683/69‑1 (MQ=255)
ccAACGGGTCCTGCATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAc > 1:1362180/1‑66 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:2055500/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:208525/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:2032930/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:1921358/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:1906537/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:1888725/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:2094078/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:2175618/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:2615714/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:2837152/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:3277311/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:1524470/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:3278129/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:3305128/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:3348225/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:407750/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:1097778/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAcca > 1:1061644/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAcca > 1:1347491/1‑67 (MQ=255)
ccAACGGGTCCTGAATCGTTTTCGCCAGATAGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCAccag > 1:2552799/1‑67 (MQ=255)
ttCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCACCAGCGCCACCg > 1:1721078/1‑57 (MQ=255)
ttCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCACCAGCGCCACCGGtc > 1:2660341/1‑59 (MQ=255)
ttCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCACCAGCGCCACCGGtc > 1:33977/1‑59 (MQ=255)
ttCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCACCAGCGCCACCGGtc > 1:429299/1‑59 (MQ=255)
ttCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCACCAGCGCCACCGGtc > 1:2619361/1‑59 (MQ=255)
ttCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCACCAGCGCCACCGGtc > 1:1650846/1‑59 (MQ=255)
ttCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCACCAGCGCCACCGGtc > 1:2516616/1‑59 (MQ=255)
ttCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCACCAGCGCCACCGGTCGTGACCAgc > 1:1018029/1‑68 (MQ=255)
ttCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCACCAGCGCCACCGGTCGTGACCAgc > 1:3153869/1‑68 (MQ=255)
ttCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCACCAGCGCCACCGGTCGTGACCAgc > 1:539401/1‑68 (MQ=255)
ttCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCACCAGCGCCACCGGTCGTGACCAgc > 1:1455811/1‑68 (MQ=255)
ttCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATCTGCCCACCAGCGCCACCGGTCGTGACCAgc > 1:2173373/1‑68 (MQ=255)
ttCGCCAGATCGGTAACCTGAATCTGCGTCGGGTCAATATGCCCACCAGCGCCACCGGtc > 1:3052363/1‑59 (MQ=255)
tGAATCTGCGTCGGATCAATCTGCCCACCCGCGCCACCGGTTGTGAcc > 1:2327208/1‑48 (MQ=255)
tGAATCTGCGTCGGATCAATCTGCCCACCCGCGCCACCGGTTGTGACCAGTGGGATTTTATTGCGCCg > 1:966495/1‑68 (MQ=255)
tGAATCTGCGTCGGATCAATCTGCCCACCCGCGCCACCGGTTGTGACCAGTGGGATTTTATTGCGCCg > 1:2034413/1‑68 (MQ=255)
tGAATCTGCGTCGGATCAATCTGCCCACCCGCGCCACCGGTTGTGACCAGTGGGATTTTATTGCGCCg > 1:1229570/1‑68 (MQ=255)
tGAATCTGCGTCGGATCAATCTGCCCACCCGCGCCACCGGTTGTGACCAGTGGGATTTTATTGCGCCg > 1:1793086/1‑68 (MQ=255)
gAATCTGCGTCGGATCAATCTGCCCACCCGCGCCACCGGTTGCGACCAGTGGGATTTTATTGCGCCGAc < 1:15922/69‑1 (MQ=255)
ggATCAATCTGCCCACCCGCGCCACCGGTTGTGACCAGTGGGATTTTATTGCGCCGACAATAAGCAATc < 1:1466977/69‑1 (MQ=255)
ggATCAATCTGCCCACCCGCGCCACCGGTTGTGACCAGTGGGATTTTATTGCGCCGACAATAAGCAATc < 1:1645942/69‑1 (MQ=255)
|
CGCCAGCGGGTCCTGAATCGTTTTCGCCAGATCGGTAACCTGAATCTGCGTCGGATCAATCTGCCCACCCGCGCCACCGGTTGTGACCAGTGGGATTTTATTGCGCCGACAATAAGCAATC > minE/1892346‑1892466
|
| 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
