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 F17 I0 R2
|
278 |
43.2 |
2215644 |
94.6% |
2095999 |
61.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,352,427 |
T→C |
25.6% |
N101D (AAC→GAC) |
thiD ← |
bifunctional hydroxy‑methylpyrimidine kinase and hydroxy‑phosphomethylpyrimidine kinase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,352,427 | 0 | T | C | 25.6%
| 64.8
/ 23.4
| 39 | N101D (AAC→GAC) | thiD | bifunctional hydroxy‑methylpyrimidine kinase and hydroxy‑phosphomethylpyrimidine kinase |
| Reads supporting (aligned to +/- strand): ref base T (13/16); new base C (6/4); total (19/20) |
| Fisher's exact test for biased strand distribution p-value = 4.80e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CGCCGAAGGTGAAAGCAGCGGGTCGCCGCTTTTTGCCAGCATAACGGTGTCGAGTACCACGTTTTGGATCTGATAACGTTGCAACCGTTCTGCCACCGCTTCAACAATATCGGTTTCCGCCAGCATACCGA > minE/1352365‑1352495
|
cgccgAAGGTGAAAGCAGCGGGTCGCCGCTTTTTGCCAGCATAACGGTGTCGAGTACCACGTCTTGGATCt > 1:1835902/1‑71 (MQ=255)
gccgAAGGTGAAAGCAGCGGGTCGCCGCTTTTTGCCAGCATAACGGTGTCGAGTACCACGTTTTGGATCTg < 1:2137495/71‑1 (MQ=255)
gccgAAGGTGAAAGCAGCGGGTCGCCGCTTTTTGCCAGCATAACGGTGTCGAGTACCACGTTTTGGATCTg < 1:170944/71‑1 (MQ=255)
gAAGGTGAAAGCAGCGGGTCGCCGCTTTTTGCCAGCATAACGGTGTCGAGTACCACGTCTTGGa > 1:1934017/1‑64 (MQ=255)
tGAAAGCAGCGGGTCGCCGCTTTTTGCCAGCATAACGGTGTCGAGTACCACGTCTTGGATCTGATAACGtt < 1:1372271/71‑1 (MQ=255)
tGAAAGCAGCGGGTCGCCGCTTTTTGCCAGCATAACGGTGTCGAGTACCACGTCTTGGATCTGATAACGtt < 1:1908280/71‑1 (MQ=255)
aaaGCAGCGGGTCGCCGCTTTTTGCCAGCATAACGGTGTCGAGTACCACGTTTTGGATCTGATAACGTTg > 1:1023425/1‑70 (MQ=255)
aaaGCAGCGGGTCGCCGCTTTTTGCCAGCATAACGGTGTCGAGTACCACGTTTTGGATCTGATAACGTTg > 1:1482358/1‑70 (MQ=255)
gcagcGGGTCGCCGCTTTTTGCCAGCATAACGGTGTCGAGTACCACGTTTTGGATCTGATAACGTTGCAAc > 1:2125666/1‑71 (MQ=255)
gTCGCCGCTTTTTGCCAGCATAACGGTGTCGAGTACCACGTTTTGGATCTg < 1:151815/51‑1 (MQ=255)
cgcTTTTTGCCAGCATAACGGTGTCGAGTACCACGTCTTGGATCTGATaa > 1:2035533/1‑50 (MQ=255)
gcTTTTTGCCAGCATAACGGTGTCGAGTACCACGTTTTGGATCTGATAACGTTGCAACCGTTCTGCCACCg < 1:614438/71‑1 (MQ=255)
gcTTTTTGCCAGCATAACGGTGTCGAGTACCACGTCTTGGATCTGATAACGTTGCAACCGTTCTGCCAcc > 1:1805396/1‑70 (MQ=255)
cTTTTTGCCAGCATAACGGTGTCGAGTACCACGTTTTGGa > 1:1344315/1‑40 (MQ=255)
ttttGCCAGCATAACGGTGTCGAGTACCACGTTTTgg < 1:411251/37‑1 (MQ=255)
tttGCCAGCATAACGGTGTCGAGTACCACGTTTTGGATCTGATAACGTTGCAACCGTTc > 1:1070750/1‑59 (MQ=255)
ccAGCATAACGGTGTCGAGTACCACGTTTTGGATCTGATAACGTTGCAACCGTTCTGCCACCGCTTcaac < 1:290236/70‑1 (MQ=255)
ccAGCATAACGGTGTCGAGTACCACGTCTTGGATCTGATAACGTTGCAACCGTTCTGCCACCGCTTcaac < 1:216263/70‑1 (MQ=255)
cATAACGGTGTCGAGTACCACGTTTTGGATCTGATaa < 1:243265/37‑1 (MQ=255)
cATAACGGTGTCGAGTACCACGTTTTGGATCTGATAACGTTGCAACCGTTCTGCCACCGCTTCAACAatat < 1:126510/71‑1 (MQ=255)
aTAACGGTGTCGAGTACCACGTTTTGGATCTGATAACGt > 1:567734/1‑39 (MQ=255)
aTAACGGTGTCGAGTACCACGTTTTGGATCTGATAACGt > 1:524177/1‑39 (MQ=255)
aTAACGGTGTCGAGTACCACGTTTTGGATCTGATAACGt > 1:570290/1‑39 (MQ=255)
aTAACGGTGTCGAGTACCACGTTTTGGATCTGATAACGt > 1:32734/1‑39 (MQ=255)
tAACGGTGTCGAGTACCACGTTTTGGATCTGATAACGTTGCAACCGTTCTGCCACCGCTTCAACAATATCg < 1:563149/71‑1 (MQ=255)
aCGGTGTCGAGTACCACGTCTTGGATCTGATAACGTTGCAACCGTTCTGCCACCGCTTCAACAATATCGGt > 1:589192/1‑71 (MQ=255)
cGGTGTCGAGTACCACGTTTTGGATCTGATAACGTTGCAACCGTTCTGCCACCGCTTCAACAATATCGGtt < 1:1218028/71‑1 (MQ=255)
cGGTGTCGAGTACCACGTCTTGGATCTGATAACGTTGCAACCGTTCTGCCACCGCTTCAACAATATCGGtt < 1:363773/71‑1 (MQ=255)
ggTGTCGAGTACCACGTTTTGGATCTGATAACGTTGCAACCGTTCTGCCACCGCTTCAACAATATCGGttt < 1:73441/71‑1 (MQ=255)
gAGTACCACGTCTTGGATCTGATAACGTTGCAACCGTTCTGCCACCGCTTCAACAATATCGGTTTCCGc > 1:512621/1‑69 (MQ=255)
aGTACCACGTTTTGTATCTGATAACGTTGCAACCGTTCTGCCACCGCTTCAACAATATCGGTTTCCGCCAg < 1:1638843/71‑1 (MQ=255)
aGTACCACGTTTTGGATCTGATAACGTTGCAACCGTTCTGCCACCGCTTCAACAATATCGGTTTCCGCCAg < 1:1119440/71‑1 (MQ=255)
aGTACCACGTTTTGGATCTGATAACGTTGCAACCGTTCTGCCACCGCTTCAACAATATCGGTTTCCGCCAg < 1:1425602/71‑1 (MQ=255)
aGTACCACGTTTTGGATCTGATAACGTTGCAACCGTTCTGCCACCGCTTCAACAATATCGGTTTCCGCCAg < 1:1648787/71‑1 (MQ=255)
cACGTTTTGGATCTGATAACGTTGCAACCGTTCTGCCACCGCTTCAACAATATCGGt < 1:916740/57‑1 (MQ=255)
aCGTTTTGGATCTGATAACGTTGCAACCGTTCTGCCACCGCTTCAACAATATCGGTTTCCGCCAGCATAcc > 1:619417/1‑71 (MQ=255)
cGTTTTGGATCTGATAACGTTGCAACCGTTCTGCCAc > 1:2206995/1‑37 (MQ=255)
gTTTTGGATCTGATAACGTTGCAACCGTTCTGCCACCGCTTCAACAATATCGGttt > 1:2179396/1‑56 (MQ=255)
gTTTTGGATCTGATAACGTTGCAACCGTTCTGCCACCGCTTCAACAATATCGGttt > 1:871708/1‑56 (MQ=255)
ttttGGATCTGATAACGTTGCAACCGTTCTGCCACCGCtt < 1:1744838/40‑1 (MQ=255)
ttttGGATCTGATAACGTTGCAACCGTTCTGCCACCGCTTCAACAATATCGGTTTCCGCCAGCATACCGa < 1:527600/70‑1 (MQ=255)
ttttGGATCTGATAACGTTGCAACCGTTCTGCCACCGCTTCAACAATATCGGTTTCCGCCAGCATACCGa < 1:354576/70‑1 (MQ=255)
ttttGGATCTGATAACGTTGCAACCGTTCTGCCACCGCTTCAACAATATCGGTTTCCGCCAGCATACCGa < 1:1755185/70‑1 (MQ=255)
|
CGCCGAAGGTGAAAGCAGCGGGTCGCCGCTTTTTGCCAGCATAACGGTGTCGAGTACCACGTTTTGGATCTGATAACGTTGCAACCGTTCTGCCACCGCTTCAACAATATCGGTTTCCGCCAGCATACCGA > minE/1352365‑1352495
|
| 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
