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 |
3,194,164 |
T→C |
100% |
T416A (ACG→GCG) |
rfaE ← |
fused heptose 7‑phosphate kinase and heptose 1‑phosphate adenyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,194,164 | 0 | T | C | 91.2%
| 101.1
/ 1.5
| 34 | T416A (ACG→GCG) | rfaE | fused heptose 7‑phosphate kinase and heptose 1‑phosphate adenyltransferase |
| Reads supporting (aligned to +/- strand): ref base T (0/3); new base C (17/14); total (17/17) |
| Fisher's exact test for biased strand distribution p-value = 2.27e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.50e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TATAGTCGCCGCCTTTCACCAGCAGATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGTGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTCCAGTGCGCCCAGCACAATCATACGCTGTTCG > W3110S.gb/3194104‑3194231
|
tataGTCGCCGCCTTTCACCAGCAGATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTc > 1:3553659/1‑70 (MQ=255)
gTCGCCGCCTTTCACCAGCAGATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGTGTCCTCTTCAAAc < 1:3517255/70‑1 (MQ=255)
gTCGCCGCCTTTCACCAGCAGATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGTGTCCTCTTCAAAc < 1:258001/70‑1 (MQ=255)
gTCGCCGCCTTTCACCAGCAGATCTGGCAAGATCCCGGCGATCAAGCGCTACGGCGTGTCCTCTTCAAAc < 1:2520494/70‑1 (MQ=255)
tCGCCGCCTTTCACCAGCAGATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGa < 1:1436851/71‑1 (MQ=255)
gccgccTTTCACCAGCAGATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGaca > 1:101567/1‑71 (MQ=255)
gccgccTTTCACCAGCAGATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGaca > 1:2843648/1‑71 (MQ=255)
agcagATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGAc < 1:3229907/71‑1 (MQ=255)
agcagATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGAc < 1:2072213/71‑1 (MQ=255)
agcagATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGAc < 1:2417289/71‑1 (MQ=255)
agcagATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCCCTTCAAACGACACTACCCAGTCGAc < 1:3280604/71‑1 (MQ=255)
agATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTc < 1:1580229/41‑1 (MQ=255)
gATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCt < 1:1487561/71‑1 (MQ=255)
aTCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGa < 1:945186/51‑1 (MQ=255)
aTCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGa < 1:2940921/51‑1 (MQ=255)
tCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGa < 1:1998089/50‑1 (MQ=255)
cTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGaca > 1:1948769/1‑51 (MQ=255)
cTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTc > 1:2797632/1‑70 (MQ=255)
cTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTc > 1:1986181/1‑70 (MQ=255)
cTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTc > 1:1547310/1‑70 (MQ=255)
cTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTc > 1:1438461/1‑70 (MQ=255)
cTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTc > 1:3111196/1‑70 (MQ=255)
tGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGa < 1:980469/48‑1 (MQ=255)
tGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGa < 1:293032/48‑1 (MQ=255)
cAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTCCAGTg > 1:552651/1‑71 (MQ=255)
aTCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTCCAGTGCGcc < 1:1887265/71‑1 (MQ=255)
aTCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTCCAGTGCGcc < 1:589539/71‑1 (MQ=255)
aTCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTCCAGTGCGcc > 1:1463572/1‑71 (MQ=255)
cAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCa > 1:2656222/1‑39 (MQ=255)
cAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTCCAg > 1:2989269/1‑54 (MQ=255)
cAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTCCAg > 1:3579250/1‑54 (MQ=255)
cAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTCCAGTGCGCCCAGCATAATCa > 1:1113843/1‑71 (MQ=255)
cAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTCCAGTGCGCCCAGCACAATCa > 1:3280622/1‑71 (MQ=255)
cAAGAGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTCCAg > 1:404040/1‑54 (MQ=255)
gcgcGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTCCAGTGCGCCCAGCACAATCATACGCTGTTCg < 1:346503/71‑1 (MQ=255)
gcgcGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTCCAGTGCGCCCAGCACAATCATACGCTGTTCg < 1:3655692/71‑1 (MQ=255)
|
TATAGTCGCCGCCTTTCACCAGCAGATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGTGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTCCAGTGCGCCCAGCACAATCATACGCTGTTCG > W3110S.gb/3194104‑3194231
|
| 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
