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 F21 I0 R2
|
308 |
27.9 |
1975068 |
96.7% |
1909890 |
67.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,573,836 |
A→G |
63.2% |
V200A (GTG→GCG) |
yihN ← |
predicted transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,573,836 | 0 | A | G | 63.2%
| 35.5
/ 35.2
| 38 | V200A (GTG→GCG) | yihN | predicted transporter |
| Reads supporting (aligned to +/- strand): ref base A (12/2); new base G (12/12); total (24/14) |
| Fisher's exact test for biased strand distribution p-value = 3.92e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TTGTCTTTCAGCACCGAGGTCATACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCACCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAAATAATAATGCCTACGGC > W3110S.gb/3573779‑3573897
|
ttGTCTTTCAGCACCGAGGTCATACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCACCTCaa > 1:1011657/1‑64 (MQ=255)
ttGTCTTTCAGCACCGAGGTCATACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCACCTCaa > 1:1559184/1‑64 (MQ=255)
ttGTCTTTCAGCACCGAGGTCATACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCACCTCaa > 1:431508/1‑64 (MQ=255)
ttGTCTTTCAGCACCGAGGTCATACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCACCTCaa > 1:347278/1‑64 (MQ=255)
ttGTCTTTCAGCACCGAGGTCATACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCACCTCaa > 1:1904811/1‑64 (MQ=255)
ttGTCTTTCAGCACCGAGGTCATACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCACCTCa > 1:1362193/1‑63 (MQ=255)
tCTTTCAGCACCGAGGTCATACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGc < 1:253416/71‑1 (MQ=255)
tCTTTCAGCACCGAGGTCATACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGc < 1:1899387/71‑1 (MQ=255)
ctgctgTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGa > 1:505257/1‑70 (MQ=255)
cTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGa > 1:1776058/1‑70 (MQ=255)
cTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGa > 1:1890552/1‑70 (MQ=255)
cTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGa > 1:1303777/1‑70 (MQ=255)
cTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGa > 1:1213462/1‑70 (MQ=255)
cTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGa > 1:1154415/1‑70 (MQ=255)
cTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCACCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGa > 1:1928554/1‑70 (MQ=255)
cTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCACCTCAACGGACGGTGCCTCTTCTTTGTCATTAAGGa > 1:1908776/1‑70 (MQ=255)
ggTGTTTTTCGATGCTCCGTCTTCTTTTTTCACCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACa > 1:970314/1‑70 (MQ=255)
tttCGATGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGaaaa > 1:1476706/1‑71 (MQ=255)
tttCGATGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGaaaa > 1:1454101/1‑71 (MQ=255)
tttCGATGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGaaa > 1:158793/1‑70 (MQ=255)
tttCGATGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGaaa > 1:643014/1‑70 (MQ=255)
gATGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAaataat < 1:880554/71‑1 (MQ=255)
gATGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAaataat < 1:1407957/71‑1 (MQ=255)
gATGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAaataat < 1:817175/71‑1 (MQ=255)
gATGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAaataat < 1:700554/71‑1 (MQ=255)
gATGCTCCGTCTTCTTTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAaataat < 1:1234842/71‑1 (MQ=255)
tcttctTTTTTCGCCTC‑ACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAAATAATAATGCCTACg < 1:551772/71‑1 (MQ=255)
cttTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAAATAATAATGCCTACg < 1:1776079/68‑1 (MQ=255)
cttTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAAATAATAATGCCTACg < 1:537654/68‑1 (MQ=255)
cttTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAAATAATAATGCCTACGGc < 1:1089450/70‑1 (MQ=255)
cttTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAAATAATAATGCCTACGGc > 1:660005/1‑70 (MQ=255)
cttTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAAATAATAATGCCTACGGc < 1:1277168/70‑1 (MQ=255)
cttTTTTCGCCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAAATAATAATGCCTACGGc > 1:152620/1‑70 (MQ=255)
cttTTTTCACCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAAATAATAATGCCTACGGc > 1:1243722/1‑70 (MQ=255)
cttTTTTCACCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAAATAATAATGCCTACGGc > 1:1267652/1‑70 (MQ=255)
cttTTTTCACCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAAATAATAATGCCTACGGc < 1:280354/70‑1 (MQ=255)
cttTTTTCACCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAAATAATAATGCCTACGGc > 1:787978/1‑70 (MQ=255)
cttTTTTCACCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAAATAATAATGCCTACGGc < 1:1745921/70‑1 (MQ=255)
|
TTGTCTTTCAGCACCGAGGTCATACTGGTGTTTTTCGATGCTCCGTCTTCTTTTTTCACCTCAACGGACGGTGCCTCTTCTTTGTCATTCAGGACAAAGAAAATAATAATGCCTACGGC > W3110S.gb/3573779‑3573897
|
| 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
