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 |
|
A4 F21 I0 R1
|
1009 |
73.8 |
4146436 |
87.4% |
3623985 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,430,365 |
T→C |
20.3% |
I111M (ATA→ATG) |
rfe ← |
UDP‑GlcNAc:undecaprenylphosphate GlcNAc‑1‑phosphate transferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,430,365 | 0 | T | C | 20.3%
| 121.6
/ 28.2
| 59 | I111M (ATA→ATG) | rfe | UDP‑GlcNAc:undecaprenylphosphate GlcNAc‑1‑phosphate transferase |
| Reads supporting (aligned to +/- strand): ref base T (22/25); new base C (5/7); total (27/32) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.96e-01 |
CGAGCACCATCTCCCAGGAGCCAAAGATATAACCCAGGCTACTGAGATAAAGCTTGCCGAACACCATTATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGATTTTTACGCTGATATCAAAACGGTCATCCAGC > minE/2430298‑2430434
|
cGAGCACCATCTCCCAGGAGCCAAAGATATAACCCAGGCTACTGAGATAAAGCTTGCCGAACACcatcat < 1:1972899/70‑1 (MQ=255)
aGCACCATCTCCCAGGAGCCAAAGATATAACCCAGGCTACTGAGATAAAGCTTGCCGAACACCATTATaa > 1:3638212/1‑70 (MQ=255)
gCACCATCTCCCAGGAGCCAAAGATATAACCCAGGCTACTGAGATAAAGCTTGCCGAACACCATTATAACa < 1:535337/71‑1 (MQ=255)
cACCATCTCCCAGGAGCCAAAGATATAACCCAGGCTACTGAGATAAAGCTTGCCGAACACCATCATAACaa < 1:2709079/71‑1 (MQ=255)
aTCTCCCAGGAGCCAAAGATATAACCCAGGCTACTGAGATAAAGCTTGCCGAACACCATTATAACAATGcc < 1:3852260/71‑1 (MQ=255)
aTCTCCCAGGAGCCAAAGATATAACCCAGGCTACTGAGATAAAGCTTGCCGAACACCATTATAACAATGc > 1:2324286/1‑70 (MQ=255)
aTCTCCCAGGAGCCAAAGATATAACCCAGGCTACTGAGATAAAGCTTGCCGAACACCATCATAACAATGcc < 1:2193013/71‑1 (MQ=255)
tctcCCAGGAGCCAAAGATATAACCCAGGCTACTGAGATAAAGCTTGCCGAACACCATTATAACAATGcc > 1:1684206/1‑70 (MQ=255)
tcCCAGGAGCCAAAGATATAACCCAGGCTACTGAGATAAAGCTTGCCGAACACCATCATAACAATGCCaa > 1:801714/1‑70 (MQ=255)
ccAGGAGCCAAAGATATAACCCAGGCTACTGAGATAAAGCTTGCCGAACACCATTATAACAATGCCa < 1:851718/67‑1 (MQ=255)
ccAGGAGCCAAAGATATAACCCAGGCTACTGAGATAAAGCTTGCCGAACACCATTATAACAATGCCa < 1:640008/67‑1 (MQ=255)
ccAGGAGCCAAAGATATAACCCAGGCTACTGAGATAAAGCTTGCCGAACACCATTATAACAATGCCAACAg > 1:755134/1‑71 (MQ=255)
gAGCCAAAGATATAACCCAGGCTACTGAGATAAAGCTTGCCGAACACCATTATAACAATGCCAACAGCGGc < 1:3335684/71‑1 (MQ=255)
ccAAAGATATAACCCAGGCTACTGAGATAAAGCTTGCCGAACACCATTATAACAATGcc < 1:2157545/59‑1 (MQ=255)
cAAAGATATAACCCAGGCTACTGAGATAAAGCTTGCCGAACACCATtata < 1:4018712/50‑1 (MQ=255)
cAAAGATATAACCCAGGCTACTGAGATAAAGCTTGCCGAACACCATTATAACAATGCCAACAGCGGCCTg < 1:2435460/70‑1 (MQ=255)
aGATATAACCCAGGCTACTGAGATAAAGCTTGCCGAACACCATTATAACAATGCCAACAGCGGc < 1:3667638/64‑1 (MQ=255)
ataACCCAGGCTACTGAGATAAAGCTTGCCGAACACCATtat > 1:2348637/1‑42 (MQ=255)
ataACCCAGGCTACTGAGATAAAGCTTGCCGAACACCATTATAACAATGCCaa > 1:711358/1‑53 (MQ=255)
ataACCCAGGCTACTGAGATAAAGCTTGCCGAACACCATTATAACAATGCCaa > 1:1452326/1‑53 (MQ=255)
taACCCAGGCTACTGAGATAAAGCTTGCCGAACACCATTATAACAATGCCAACAGCGGCCTGTATGGTGGc < 1:1211150/71‑1 (MQ=255)
aaCCCAGGCTACTGAGATAAAGCTTGCCGAACACCATTATAACaa > 1:3679981/1‑45 (MQ=255)
aCCCAGGCTACTGAGATAAAGCTTGCCGAACACCATCATAACAATGCCaa > 1:1664153/1‑50 (MQ=255)
cccAGGCTACTGAGATAAAGCTTGCCGAACACCATCATAACAATGCCAACAGCGGCCTGTATGGTGGCACg > 1:817342/1‑71 (MQ=255)
aGGCTACTGAGATAAAGCTTGCCGAACACCATTATAAc < 1:3267636/38‑1 (MQ=255)
tACTGAGATAAAGCTTGCCGAACACCATTATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGAtttt > 1:1768805/1‑70 (MQ=255)
cTGAGATAAAGCTTGCCGAACACCATTATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGAtttt < 1:2227868/68‑1 (MQ=255)
cTGAGATAAAGCTTGCCGAACACCATCATAACAAt < 1:812836/35‑1 (MQ=255)
gagaTAAAGCTTGCCGAACACCATTATAACAATGCCAACAGCGGCCTGTa > 1:1101803/1‑50 (MQ=255)
gagaTAAAGCTTGCCGAACACCATCATAACAATgg > 1:3872973/1‑34 (MQ=39)
gagaTAAAGCTTGCCGAACACCATCATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGAtttt < 1:387455/66‑1 (MQ=255)
agaTAAAGCTTGCCGAACACCATTATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGATTTTTACg < 1:252153/69‑1 (MQ=255)
agaTAAAGCTTGCCGAACACCATTATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGATTTTTACGCt < 1:3053866/71‑1 (MQ=255)
agaTAAAGCTTGCCGAACACCATTATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGATTTTTACGCt > 1:312336/1‑71 (MQ=255)
agaTAAAGCTTGCCGAACACCATTATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGATTTTTACGCt > 1:3149675/1‑71 (MQ=255)
agaTAAAGCTTGCCGAACACCATTATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGATTTTTACGCt > 1:2446346/1‑71 (MQ=255)
agaTAAAGCTTGCCGAACACCATCATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGATTTTTACGCt < 1:2099386/71‑1 (MQ=255)
aTAAAGCTTGCCGAACACCATTATAACAATGCCAACAGCGGCCTGTAt < 1:3105234/48‑1 (MQ=255)
aTAAAGCTTGCCGAACACCATTATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGATTTTTACGCt < 1:2857188/69‑1 (MQ=255)
aaaGCTTGCCGAACACCATTATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGATTTTTACGCTGata > 1:1112984/1‑71 (MQ=255)
aaGCTTGCCGAACACCATTATAACAATGCCAACAGCGGCCTGt < 1:1264065/43‑1 (MQ=255)
aaGCTTGCCGAACACCATTATAACAATGCCAACAGCGGCCTGt < 1:231657/43‑1 (MQ=255)
aaGCTTGCCGAACACCATCATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGATTTTTACGCTg > 1:2964362/1‑67 (MQ=255)
aGCTTGCCGAACACCATTATAACAATGCCAACAGCGGCCTGTa > 1:266745/1‑43 (MQ=255)
gCTTGCCGAACACCATTATAACAATGCCAACAGCGGCCTGTAt > 1:3970121/1‑43 (MQ=255)
gCTTGCCGAACACCATTATAACAATGCCAACAGCGGCCTGTAt > 1:3974846/1‑43 (MQ=255)
gCTTGCCGAACACCATCATAACAATGCCAACAGCGGCCTGTATGGTGGCACgg < 1:3915310/53‑1 (MQ=255)
cTTGCCGAACACCATTATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGAtt < 1:453657/55‑1 (MQ=255)
cTTGCCGAACACCATTATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGAtt < 1:4109656/55‑1 (MQ=255)
cTTGCCGAACACCATTATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGATTTTTa > 1:3129362/1‑59 (MQ=255)
cTTGCCGAACACCATTATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGATTTTTACGCTGATATCaa < 1:1441489/71‑1 (MQ=255)
ttGCCGAACACCATTATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGATTTTTACGCt < 1:1273013/62‑1 (MQ=255)
ccGAACACCATTATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGATTTTTACGCTGATATCAAAACg < 1:999760/71‑1 (MQ=255)
ccGAACACCATTATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGATTTTTACGCTGATATCAAAACg > 1:139623/1‑71 (MQ=255)
ccGAACACCATCATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGATTTTTACGCTGATATCAAAACg < 1:2310147/71‑1 (MQ=255)
cGAACACCATTATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGATTTTTACGCTGATATCAAAACgg < 1:511115/71‑1 (MQ=255)
cGAACACCATTATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGATTTTTACGCTGATATCAAAACgg < 1:3132776/71‑1 (MQ=255)
aaCACCATTATAACAATGCCAACAGCGGCCTGTATGGTGGCa > 1:3342597/1‑42 (MQ=255)
aaCACCATTATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGATTTTTACg > 1:3411496/1‑54 (MQ=255)
aaCACCATTATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGATTTTTACGCTGatat < 1:2618568/61‑1 (MQ=255)
cacCATTATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGATTTTTACGCTGATATCAAAACGGTAAt > 1:2073666/1‑71 (MQ=255)
ccATTATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGATTTTTACGCTGATATCAAAACGGTCATc > 1:3572934/1‑70 (MQ=255)
ttATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGATTTTTACGCTGa > 1:2907773/1‑51 (MQ=255)
ttATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGATTTTTACGCTGATATCAAAACGGTCATCCAgc > 1:3904854/1‑71 (MQ=255)
ttATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGATTTTTACGCTGATATCAAAACGGTCATCCAgc > 1:3565195/1‑71 (MQ=255)
|
CGAGCACCATCTCCCAGGAGCCAAAGATATAACCCAGGCTACTGAGATAAAGCTTGCCGAACACCATTATAACAATGCCAACAGCGGCCTGTATGGTGGCACGGATTTTTACGCTGATATCAAAACGGTCATCCAGC > minE/2430298‑2430434
|
| 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
