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 |
|
A1 F8 I0 R2
|
422 |
46.8 |
3726540 |
94.7% |
3529033 |
61.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,916,386 |
G→A |
100% |
E892K (GAA→AAA) |
barA → |
hybrid sensory histidine kinase, in two‑component regulatory system with UvrY |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,916,386 | 0 | G | A | 86.0%
| 127.0
/ 13.4
| 50 | E892K (GAA→AAA) | barA | hybrid sensory histidine kinase, in two‑component regulatory system with UvrY |
| Reads supporting (aligned to +/- strand): ref base G (2/5); new base A (17/26); total (19/31) |
| Fisher's exact test for biased strand distribution p-value = 6.95e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01 |
| Rejected as polymorphism: Polymorphic base substitution creates a homopolymer stretch. |
TATAGCGGTGTGCCACGTATGAAGAATCTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAAGAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTGGACGAGATGGATAATGTCGCGCGCGAA > W3110S.gb/2916317‑2916448
|
tataGCGGTGTGCCACGTATGAAGAATCTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAaag > 1:3593709/1‑70 (MQ=255)
taGCGGTGTGCCACGTATGAAGAATCTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAaaga < 1:1976922/69‑1 (MQ=255)
cGGTGTGCCACGTATGAAGAATCTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAaaaaagaag < 1:2950293/71‑1 (MQ=255)
cGGTGTGCCACGTATGAAGAATCTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAaaaaagaag < 1:2800270/71‑1 (MQ=255)
cGGTGTGCCACGTATGAAGAATCTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAaaaaagaag < 1:1628049/71‑1 (MQ=255)
cGGTGTGCCACGTATGAAGAATCTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAaaaaagaag < 1:2252531/71‑1 (MQ=255)
gttgtgCCACGTATGAAGAATCTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAaaaagaaga < 1:635421/69‑1 (MQ=255)
ggTGTGCCACGTATGAAGAATCTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAaaaagaaga < 1:1977642/71‑1 (MQ=255)
ggTGTGCCACGTATGAAGAATCTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAaaaagaaga < 1:426361/71‑1 (MQ=255)
tgCCACGTATGAAGAATCTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGAttt < 1:1768882/70‑1 (MQ=255)
tgCCACGTATGAAGAATCTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTg > 1:280237/1‑71 (MQ=255)
ccACGTATGAAGAATCTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTgg > 1:332866/1‑70 (MQ=255)
ccACGTATGAAGAATCTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTgg > 1:2246787/1‑70 (MQ=255)
ccACGTATGAAGAATCTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTgg < 1:1133086/70‑1 (MQ=255)
ccACGTATGAAGAATCTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTgg > 1:2707357/1‑70 (MQ=255)
ccACGTATGAAGAATCTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTgg < 1:2906109/70‑1 (MQ=255)
ccACGTATGAAGAATCTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTgg > 1:2993852/1‑70 (MQ=255)
ccACGTATGAAGAATCTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTgg < 1:1396234/70‑1 (MQ=255)
ccACGTATGAAGAATCTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTgg < 1:1793764/70‑1 (MQ=255)
tGAAGAATCTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAAGAAGAAGATTTGGAACCGGAg < 1:1789543/71‑1 (MQ=255)
tGAAGAAACTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAaaaagaaga > 1:2552268/1‑58 (MQ=39)
aagaaTCTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTGGAACCGGAgct > 1:3073101/1‑71 (MQ=255)
aagaaTCTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTGGAACCGGAgct > 1:212342/1‑71 (MQ=255)
aagaaTCTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTGGAACCGGAgct > 1:1740479/1‑71 (MQ=255)
aaTCTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTGGAACCGGAgctgct > 1:1769067/1‑71 (MQ=255)
tctcTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAAGAAGAAGATTTGGAACCGGAGctgctg > 1:2599149/1‑70 (MQ=255)
tctcTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAAGAAGAAGATTTGGAACCGGAGctgctg > 1:2602485/1‑70 (MQ=255)
tctcTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTGGAACCGGAGctgctg > 1:202591/1‑70 (MQ=255)
tctcTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTGGAACCGGAGctgctg > 1:1634847/1‑70 (MQ=255)
tctcTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTGGAACCGGAGctgctg > 1:2468795/1‑70 (MQ=255)
tGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTGGAACCgg < 1:2611591/58‑1 (MQ=255)
tGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTGGAACCgg < 1:3845/58‑1 (MQ=255)
aaCTGATCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTg < 1:785777/71‑1 (MQ=255)
cTGATCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTGGAACCGGAg < 1:397140/54‑1 (MQ=255)
cTGATCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTGGAACCGGAg < 1:2119282/54‑1 (MQ=255)
tGATCGAACACCAGCTACGTAGCGGTACTAaaaaagaag > 1:2658049/1‑39 (MQ=37)
tGATCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTggtc > 1:684180/1‑69 (MQ=255)
gATCGAACAACAGCTACGTAGCGGTACTAaaaaagaag > 1:1596510/1‑38 (MQ=255)
gATCGAACAACAGCTACGTAGCGGTACTAaaaaagaag > 1:141662/1‑38 (MQ=255)
gATCGAACAACAGCTACGTAGCGGTACTAaaaaagaag > 1:504041/1‑38 (MQ=255)
gATCGAACAACAGCTACGTAGCGGTACTAaaaaagaag > 1:299087/1‑38 (MQ=255)
gATCGAACAACAGCTACGTAGCGGTACTAaaaaagaag > 1:3318914/1‑38 (MQ=255)
gATCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTgg > 1:3239149/1‑68 (MQ=255)
gATCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTGGa > 1:3134337/1‑69 (MQ=255)
aTCGAACAACAGCTACGTAGCGGTACTAAAGAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTGGACga < 1:2591566/71‑1 (MQ=255)
aTCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTGGACga < 1:93173/71‑1 (MQ=255)
aTCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTGGACga < 1:1762350/71‑1 (MQ=255)
aTCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTGGACga < 1:2432163/71‑1 (MQ=255)
tCGAACAACAGCTACGTAGCGGTACTAAAAAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTGGACga < 1:3000763/70‑1 (MQ=255)
acaacaGCTACGTAGCGGTACTAAAAAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTGGACGAGATgg < 1:2437029/71‑1 (MQ=255)
aacaGCTACGTAGCGGTACTAAAAAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTGGACGAGATGGAt < 1:1290522/71‑1 (MQ=255)
aacaGCTACGTAGCGGTACTAAAAAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTGGACGAGATGGAt < 1:772394/71‑1 (MQ=255)
aacaGCTACGTAGCGGTACTAAAAAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTGGACGAGATGGAt < 1:2697092/71‑1 (MQ=255)
aacaGCTACGTAGCGGTAATAAAAAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTGGACGAGATGTAt < 1:919062/71‑1 (MQ=255)
acaGCTACGTAGCGGTACTAAAAAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTGGACGAGATGGAt < 1:2627541/70‑1 (MQ=255)
aCGTAGCGGTACTAAAAAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTGGACGAGATGGATAATGTcg > 1:3465082/1‑71 (MQ=255)
gCGGTACTAAAAAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTGGACGAGATGGATAATGTcgcgcgg > 1:3278080/1‑70 (MQ=255)
gTACTAAAAAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTGGACGAGATGGATAATGTCGCGCGCGaa < 1:2490724/71‑1 (MQ=255)
tACTAAAAAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTGGACga < 1:343388/48‑1 (MQ=255)
tACTAAAAAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTGGACga < 1:860294/48‑1 (MQ=255)
cTAAAGAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTGGACgag < 1:3187656/47‑1 (MQ=255)
cTAAAGAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTGGACgag < 1:1730165/47‑1 (MQ=255)
cTAAAGAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTGGACgag < 1:1565210/47‑1 (MQ=255)
tAAAAAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTGGACga < 1:416979/45‑1 (MQ=255)
tAAAAAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTGGACga < 1:1725175/45‑1 (MQ=255)
tAAAAAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTGGACga < 1:496796/45‑1 (MQ=255)
aaaaaaGAAGATTTGGAACCGGAGCTGCTGGAACTg < 1:3109294/36‑1 (MQ=255)
|
TATAGCGGTGTGCCACGTATGAAGAATCTCTGCCAACTGATCGAACAACAGCTACGTAGCGGTACTAAAGAAGAAGATTTGGAACCGGAGCTGCTGGAACTGTTGGACGAGATGGATAATGTCGCGCGCGAA > W3110S.gb/2916317‑2916448
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
