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 |
2,187,412 |
A→G |
30.3% |
L149L (TTG→CTG) |
nanT ← |
sialic acid transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,187,412 | 0 | A | G | 30.3%
| 38.7
/ 19.0
| 46 | L149L (TTG→CTG) | nanT | sialic acid transporter |
| Reads supporting (aligned to +/- strand): ref base A (30/2); new base G (5/9); total (35/11) |
| Fisher's exact test for biased strand distribution p-value = 7.69e-05 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ATAGACCTGAGCGGCAACGACGGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAGATGTTTTGGCCAGCTTTCAATGACATAGGTGGCG > minE/2187365‑2187470
|
ataGACCTGAGCGGCAACGACGGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGttt > 1:1320240/1‑66 (MQ=255)
ataGACCTGAGCGGCAACGACGGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGTTa > 1:15986/1‑67 (MQ=255)
gACCTGAGCGGCAACGACGGCCCCCACAGAGAAGCCTGAAATCAAAAAAc > 1:794106/1‑50 (MQ=255)
gACCTGAGCGGCAACGACGGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACt > 1:932004/1‑54 (MQ=255)
gACCTGAGCGGCAACGACGGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGc > 1:1677893/1‑57 (MQ=255)
gACCTGAGCGGCAACGACGGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAg > 1:1007487/1‑69 (MQ=255)
gACCTGAGCGGCAACGACGGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAg > 1:2590470/1‑69 (MQ=255)
gACCTGAGCGGCAACGACGGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAg > 1:254386/1‑69 (MQ=255)
gACCTGAGCGGCAACGACGGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAg > 1:248615/1‑69 (MQ=255)
gACCTGAGCGGCAACGACGGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAg > 1:2642560/1‑69 (MQ=255)
gACCTGAGCGGCAACGACGGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAg > 1:2778338/1‑69 (MQ=255)
gACCTGAGCGGCAACGACGGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAg > 1:3072804/1‑69 (MQ=255)
gACCTGAGCGGCAACGACGGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAg > 1:3422661/1‑69 (MQ=255)
gACCTGAGCGGCAACGACGGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAg > 1:46459/1‑69 (MQ=255)
gACCTGAGCGGCAACGACGGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAg > 1:527690/1‑69 (MQ=255)
gACCTGAGCGGCAACGACGGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAg > 1:54369/1‑69 (MQ=255)
gACCTGAGCGGCAACGACGGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAg > 1:1580245/1‑69 (MQ=255)
gACCTGAGCGGCAACGACGGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAg > 1:584713/1‑69 (MQ=255)
gacgGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTg > 1:2110138/1‑46 (MQ=255)
gacgGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAGATGTTTTGGCCAGCt > 1:397084/1‑69 (MQ=255)
gacgGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAGATGTTTTGGCCAGCt > 1:2302203/1‑69 (MQ=255)
gacgGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAGATGTTTTGGCCAGCt > 1:737438/1‑69 (MQ=255)
gacgGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAGATGTTTTGGCCAGCt > 1:2635097/1‑69 (MQ=255)
gacgGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCCTTGTTACGCAGATGTTTTGGCCAGc > 1:2364701/1‑68 (MQ=255)
acgGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAGATGTTTTGGCCAGCt > 1:951724/1‑68 (MQ=255)
acgGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAGATGTTTTGGCCAGCt > 1:2595220/1‑68 (MQ=255)
acgGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAGATGTTTTGGCCAGCt > 1:2090065/1‑68 (MQ=255)
acgGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAGATGTTTTGGCCAGCt > 1:1920292/1‑68 (MQ=255)
ccccACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAGATGTTTTGGCCAGCTTTCAAt < 1:1145151/69‑1 (MQ=255)
ccACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAGATGTTTTGGCCAGCTTTCAATGa < 1:3052035/69‑1 (MQ=255)
ctgagaAGCCGGAAATCAGAAAACCACTGGCTTTGTTACTCAGATGCTTTGGCCAGCTTTCAATGACAt > 1:1812555/3‑69 (MQ=255)
ctgagaAGCCGGAAATCAGAAAACCACTGGCTTTGTTACGCAGATGCTTTGGCCAGCTTTCAATGACAt > 1:2767981/3‑69 (MQ=255)
ctgagaAGCCGGAAATCAGAAAACCACTGGCTTTGTTACGCAGATGCTTTGGCCAGCTTTCAATGACAt > 1:3005024/3‑69 (MQ=255)
ctgagaAGCCGGAAATCAGAAAACCACTGGCTTTGTTACGCAGATGCTTTGGCCAGCTTTCAATGACAt > 1:1432890/3‑69 (MQ=255)
ctgagaAGCCGGAAATCAGAAAACCACTGGCTTTGTTACGCAGATGCTTTGGCCAGCTTTCAATGACAt > 1:1453889/3‑69 (MQ=255)
gagaAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAGATGTTTTGGCCAGCTTTCaa > 1:2688798/1‑61 (MQ=255)
gagaAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAGATGTTTTGGCCAGCTTTCAATGACATAg > 1:3334648/1‑69 (MQ=255)
ggAAATCAGAAAACCACTGGCTTTGTTACGCAGATGCTTTGGCCAGCTTTCAATGACATATGTGgcg < 1:3401559/66‑1 (MQ=255)
ggAAATCAGAAAACCACTGGCTTTGTTACGCAGATGCTTTGGCCAGCTTTCAATGACATAGGTGgcg < 1:1138184/66‑1 (MQ=255)
ggAAATCAGAAAACCACTGGCTTTGTTACGCAGATGCTTTGGCCAGCTTTCAATGACATAGGTGgcg < 1:1191660/66‑1 (MQ=255)
ggAAATCAGAAAACCACTGGCTTTGTTACGCAGATGCTTTGGCCAGCTTTCAATGACATAGGTGgcg < 1:1713951/66‑1 (MQ=255)
ggAAATCAGAAAACCACTGGCTTTGTTACGCAGATGCTTTGGCCAGCTTTCAATGACATAGGTGgcg < 1:1947866/66‑1 (MQ=255)
ggAAATCAGAAAACCACTGGCTTTGTTACGCAGATGCTTTGGCCAGCTTTCAATGACATAGGTGgcg < 1:2029365/66‑1 (MQ=255)
ggAAATCAGAAAACCACTGGCTTTGTTACGCAGATGCTTTGGCCAGCTTTCAATGACATAGGTGgcg < 1:2931959/66‑1 (MQ=255)
ggAAATCAGAAAACCACTGGCTTTGTTACGCAGATGCTTTGGCCAGCTTTCAATGACATAGGTGgcg < 1:2373797/66‑1 (MQ=255)
ggAAATCAGAAAACCACTGGCTTTGTTACGCAGATGCTTTGGCCAGCTTTCAATGACATAGGTGgcg < 1:2467223/66‑1 (MQ=255)
|
ATAGACCTGAGCGGCAACGACGGCCCCCACAGAGAAGCCTGAAATCAAAAAACCACTGGCTTTGTTACGCAGATGTTTTGGCCAGCTTTCAATGACATAGGTGGCG > minE/2187365‑2187470
|
| 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
