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 |
1,988,048 |
A→G |
100% |
N190N (AAT→AAC) |
yggN ← |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,988,048 | 0 | A | G | 75.1%
| 56.4
/ 14.0
| 48 | N190N (AAT→AAC) | yggN | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (4/8); new base G (36/0); total (40/8) |
| Fisher's exact test for biased strand distribution p-value = 1.31e-06 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCT > minE/1987983‑1988112
|
tCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGCCCCCCCAGGCTTCCCAGCACATTc > 1:485668/1‑69 (MQ=255)
tCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGCCCCCCCAGGCTTCCCAGCACATTc > 1:1171556/1‑69 (MQ=255)
cTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGCCCCCCCAGGCTTCCCAGCACATTc > 1:3307528/1‑68 (MQ=255)
tCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGCCCCCCCAGGCTTCCCAGCACATTCTGt < 1:590867/66‑1 (MQ=255)
tCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGCCCCCCCAGGCTTCCCAGCACATTCTGt < 1:1550748/66‑1 (MQ=255)
tCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGCCCCCCCAGGCTTCCCAGCACATTCTGt < 1:3096975/66‑1 (MQ=255)
tCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGCCCCCCCAGGCTTCCCAGCACATTCTGt < 1:2921472/66‑1 (MQ=255)
tCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGCCCCACCAGGCTTCCCAGCACATTCTGt < 1:1497147/66‑1 (MQ=255)
ccTGCTTTTTCCACTCGGTTTGGTTTGAGGATTGCAGCCCCCCCAGGCTTCCCAGCACATTCTGt < 1:2887876/65‑1 (MQ=255)
tGGATTGAGGATTGCAGCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGc > 1:1357932/1‑69 (MQ=255)
ccgcccAGGCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCa > 1:1440397/4‑67 (MQ=255)
ccgcccAGGCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCa > 1:2284693/4‑67 (MQ=255)
ccgcccAGGCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt > 1:1053477/4‑68 (MQ=255)
ccgcccAGGCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt > 1:2933317/4‑68 (MQ=255)
ccgcccAGGCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt > 1:547857/4‑68 (MQ=255)
ccgcccAGGCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt > 1:2724675/4‑68 (MQ=255)
ccgcccAGGCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt > 1:2672707/4‑68 (MQ=255)
ccgcccAGGCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt > 1:2236931/4‑68 (MQ=255)
ccgcccAGGCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt > 1:2150003/4‑68 (MQ=255)
ccgcccAGGCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt > 1:2137462/4‑68 (MQ=255)
ccgcccAGGCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt > 1:2070887/4‑68 (MQ=255)
ccgcccAGGCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt > 1:1099170/4‑68 (MQ=255)
ccgcccAGGCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt > 1:179672/4‑68 (MQ=255)
ccgcccAGGCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt > 1:1705243/4‑68 (MQ=255)
ccgcccAGGCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt > 1:1168623/4‑68 (MQ=255)
cAGGCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCt > 1:487577/1‑39 (MQ=255)
cAGGCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCttt > 1:1294807/1‑54 (MQ=255)
cAGGCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCa > 1:656089/1‑62 (MQ=255)
cAGGCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCa > 1:3299737/1‑62 (MQ=255)
cAGGCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt > 1:980782/1‑63 (MQ=255)
cAGGCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt > 1:2860311/1‑63 (MQ=255)
cAGGCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt > 1:2852368/1‑63 (MQ=255)
cAGGCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt > 1:2538539/1‑63 (MQ=255)
cAGGCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt > 1:1623795/1‑63 (MQ=255)
cAGGCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt > 1:1980335/1‑63 (MQ=255)
cAGGCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCAt > 1:2098865/1‑63 (MQ=255)
cAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCAtt < 1:974703/69‑1 (MQ=255)
cAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCAtt < 1:3055233/69‑1 (MQ=255)
gCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAAt > 1:1990767/1‑69 (MQ=255)
gCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAAt > 1:2607244/1‑69 (MQ=255)
gCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAAt > 1:1387003/1‑69 (MQ=255)
gCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAAt > 1:1289433/1‑69 (MQ=255)
gCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAAt > 1:29943/1‑69 (MQ=255)
gCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAAt > 1:2288572/1‑69 (MQ=255)
gCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAAt > 1:1162253/1‑69 (MQ=255)
gCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAAt > 1:1022939/1‑69 (MQ=255)
gCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCGTTCGCGCCCATTTCATTAAt > 1:1853832/1‑69 (MQ=255)
gCTTCCCAGCACGTTCTGTAATGGGTTACCGCCGCGTTTCAGCACCGCTTTCGCGCCCATTTCAtt > 1:2883542/1‑66 (MQ=255)
cacaTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAAt > 1:346584/1‑60 (MQ=255)
cacaTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCt > 1:1867425/1‑68 (MQ=255)
cacaTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCt > 1:1138710/1‑68 (MQ=255)
cacaTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCt > 1:396581/1‑68 (MQ=255)
cacaTTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCt > 1:1643260/1‑68 (MQ=255)
|
TCTTTTTCCTGCTTTTTCCACTCGGTTTGGATTGAGGATTGCAGCCCCCCCAGGCTTCCCAGCACATTCTGTAATGGGTTACCGCCGCTTTTCAGCACCGCTTTCGCGCCCATTTCATTAATGCTGTCCT > minE/1987983‑1988112
|
| 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
