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 |
1,700,462 |
A→G |
31.5% |
L24P (CTA→CCA) |
hcaT ← |
predicted 3‑phenylpropionic transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,700,462 | 0 | A | G | 31.5%
| 62.8
/ 40.0
| 50 | L24P (CTA→CCA) | hcaT | predicted 3‑phenylpropionic transporter |
| Reads supporting (aligned to +/- strand): ref base A (16/18); new base G (5/10); total (21/29) |
| Fisher's exact test for biased strand distribution p-value = 5.33e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AACAGGCCGATGGTTTCTGGCGTTAAACCAATCCCTTTAAGCCAGACGCTCCAGAAAGGTAGAAAAATGCCGTAACTAAAAAAGTATGTGAAATAGCCGAGCGCCAACCAGCGCGTGGATTGCAAAACC > minE/1700402‑1700530
|
aaCAGGCCGATGGTTTCTGGCGTTAAACCAATCCCTTTAAGCCAGACGCTCCAGAAAGGTAGaaaaa > 1:1386532/1‑67 (MQ=255)
cAGGCCGATGGTTTCTGGCGTTAAACCAATCCCTTTAAGCCAGACGCTCCAGAAAGGTGGAAAAATGCCGt < 1:1438672/71‑1 (MQ=255)
cAGGCCGATGGTTTCTGGCGTTAAACCAATCCCTTTAAGCCAGACGCTCCAGAAAGGTAGAAAAATGCCGt < 1:587364/71‑1 (MQ=255)
cAGGCCGATGGTTTCTGGCGTTAAACCAATCCCTTTAAGCCAGACGCTCCAGAAAGGTAGAAAAATGCCGt < 1:1971871/71‑1 (MQ=255)
cAGGCCGATGGTTTCTGGCGTTAAACCAATCCCTTTAAGCCAGACGCTCCAGAAAGGTAGAAAAATGCCGt < 1:1840501/71‑1 (MQ=255)
aGGCCGATGGTTTCTGGCGTTAAACCAATCCCTTTAAGCCAGACGCTCCAGAAAGGTAGaaa < 1:541653/62‑1 (MQ=255)
gCCGATGGTTTCTGGCGTTAAACCAATCCCTTTAAGCCAGACGCTCCAGAAAGGTAGAAAAATGCCGTAAc > 1:245374/1‑71 (MQ=255)
tCTGGCGTTAAACCAATCCCTTTAAGCCAGACGCTCCAGAAAGGTGGAAAAATGCCGTAACTAAAAAAGTa > 1:722773/1‑71 (MQ=255)
tGGCGTTAAACCAATCCCTTTAAGCCAGACGCTCCAGAAAGGTAGAAAAATGCCGTAACTAAAAAAGTAtg > 1:2159668/1‑71 (MQ=255)
tGGCGTTAAACCAATCCCTTTAAGCCAGACGCTCCAGAAAGGTAGAAAAATGCCGTAACTAAAAAAGTAtg > 1:2157112/1‑71 (MQ=255)
ggCGTTAAACCAATCCCTTTAAGCCAGACGCTCCAGAAAGGTAGAAAAATGCCGTAACTAAAAAAGTAtgt > 1:1444929/1‑71 (MQ=255)
cGTTAAACCAATCCCTTTAAGCCAGACGCTCCAGAAAGGTGGAAAAATGCCGTaa > 1:1997381/1‑55 (MQ=255)
cGTTAAACCAATCCCTTTAAGCCAGACGCTCCAGAAAGGTAGAAAAATGCCGTAACTAAAAAAGTATGTGa < 1:255657/71‑1 (MQ=255)
gTTAAACCAATCCCTTTAAGCCAGACGCTCCAGAAAGGTAGAAAAATGCCGTAACTAAAAAAGTATGTGa < 1:19939/70‑1 (MQ=255)
ttAAACCAATCCCTTTAAGCCAGACGCTCCAGAAAGGTAGAAAAATGCCGt < 1:587135/51‑1 (MQ=255)
ttAAACCAATCCCTTTAAGCCAGACGCTCCAGAAAGGTAGAAAAATGCCGTAACTAAAAAAGt < 1:1459885/63‑1 (MQ=255)
ttAAACCAATACCTTTAAGCCAGACGCTCCAGAAAGGTAGAAAAATGCCGTAACTAAAAAAGt < 1:768751/63‑1 (MQ=255)
tAAACCAATCCCTTTAAGCCAGACGCTCCAGAAAGGTAGAAAAATGCCGTAACTAAAAAAGTATGTGaaa > 1:250842/1‑70 (MQ=255)
aaaCCAATCCCTTTAAGCCAGACGCTCCAGAAAGGTGGAAAAATGCCGTAACTAAAAAAGTATGTGaaa > 1:1961262/1‑69 (MQ=255)
aaaCCAATCCCTTTAAGCCAGACGCTCCAGAAAGGTAGAAAAATGCCGTAACTAAAAAAGTATGTGaaa > 1:545199/1‑69 (MQ=255)
aaaCCAATCCCTTTAAGCCAGACGCTCCAGAAAGGTAGAAAAATGCCGTAACTAAAAAAGTATGTGaa > 1:1193841/1‑68 (MQ=255)
ccTTTAAGCCAGACGCTCCAGAAAGGTGGAAAAATGACGTAACTAAAAAAGTATGTGAAATAGCCGAgcg > 1:797290/1‑70 (MQ=255)
tttAAGCCAGACGCTCCAGAAAGGTAGAAAAATGCCGTAACTAAAAAAGTATGTGAAATAGCCGAGCGcc > 1:1126439/1‑70 (MQ=255)
tttAAGCCAGACGCTCCAGAAAGGT‑‑AAAAATGCCGTAACTaa < 1:533534/42‑1 (MQ=38)
tAAGCCAGACGCTCCAGAAAGGTAGAAAAATGCCGTAACTAAAAAAGTATGTGAAATAGCCGAGCGCCAAc > 1:1860810/1‑71 (MQ=255)
gCCAGACGCTCCAGAAAGGTGGAAAAATGCCGTAACTAAAAAAGTATGTGAAATAGCCGAGCGCCAACCAg < 1:25501/71‑1 (MQ=255)
cAGACGCTCCAGAAAGGTAGAAAAATGCCGTAACTAAAAAAGTATGTGAAATAGCCGAGCGCCAACCAgcg < 1:591923/71‑1 (MQ=255)
aGACGCTCCAGAAAGGTAGAAAAATGCCGTAACTAAAAAAGTATGTGaa < 1:742297/49‑1 (MQ=255)
gACGCTCCAGAAAGGTAGAAAAATGCCGTAACTAAAAAAGTATGTGAAATAGCCGAGCGCCAACCAgcgc > 1:768262/1‑70 (MQ=255)
aCGCTCCAGAAAGGTAGAAAAATGCCGTAACTAAAAAAGTATGTGAAATAGCCGAGCGCCAACCAGCGCGt > 1:506149/1‑71 (MQ=255)
cGCTCCAGAAAGGTGGAAAAATGCCGTAACTAAAAAAGTATGTGAAATAGCCGAGCGCCAACCAGCGCGTg < 1:2068467/71‑1 (MQ=255)
cTCCAGAAAGGTGGAAAAATGACGTAACTAAAAAAGTATGTGa < 1:1148369/43‑1 (MQ=38)
tCCAGAAAGGTGGAAAAATGCCGTAACTAAAAAAGTAtgtg < 1:1461608/41‑1 (MQ=255)
tCCAGAAAGGTGGAAAAATGCCGTAACTAAAAAAGTAtgtg < 1:2133681/41‑1 (MQ=255)
tCCAGAAAGGTGGAAAAATGCCGTAACTAAAAAAGTAtgtg < 1:1822595/41‑1 (MQ=255)
tCCAGAAAGGTAGAAAAATGCCGTAACTAAAAAAGTATGTGa < 1:769893/42‑1 (MQ=255)
ccAGAAAGGTAGAAAAATGCCGTAACTAAAAAAGTATGTGAAATAGCCGAGCGCCAACCAGCGCGTGGa > 1:1130441/1‑69 (MQ=255)
ccAGAAAGGTAGAAAAATGCCGTAACTAAAAAAGTATGTGAAATAGCCGAGCGCCAACCAGCGCGTGGa > 1:1804574/1‑69 (MQ=255)
cAGAAAGGTAGAAAAATGCCGTAACTAAAAAAGTATGTGAAATAGCCGAGCGCCAACCAGCGCGTg < 1:344505/66‑1 (MQ=255)
cAGAAAGGTAGAAAAATGCCGTAACTAAAAAAGTATGTGAAATAGCCGAGCGCCAACCAGCGCGTg < 1:1194415/66‑1 (MQ=255)
cAGAAAGGTAGAAAAATGCCGTAACTAAAAAAGTATGTGAAATAGCCGAGCGCCAACCAGCGCGTGGAt < 1:142503/69‑1 (MQ=255)
aGAAAGGTAGAAAAATGCCGTAACTAAAAAAGTATGTGa < 1:1931445/39‑1 (MQ=255)
gAAAGGTGGAAAAATGCCGTAACTAAAAAAGTATGTGAAATAGCCGAGCGcc > 1:165051/1‑52 (MQ=255)
aaaGGTGGAAAAATGCCGTAACTAAAAAAGTAtgtg < 1:724675/36‑1 (MQ=255)
aaaGGTAGAAAAATGCCGTAACTAAAAAAGTATGTGAAATAGCCGAGCGCCAACCAGCGCGTGGATTGCaa < 1:1610349/71‑1 (MQ=255)
aaGGTAGAAAAATGGCGTAACTAAAAAAGTATGTGAAATAGCCGa > 1:747662/1‑45 (MQ=255)
aaGGTAGAAAAATGCCGTAACTAAAAAAGTATGTGAAATAGCCGAGCGcc > 1:598886/1‑50 (MQ=255)
ggTGGAAAAATGCCGTAACTAAAAAAGTATGTGAAATAGCCGAGCGCCAACCAGCGCGTGGATTGCAAAAc < 1:651368/71‑1 (MQ=255)
ggTGGAAAAATGCCGTAACTAAAAAAGTATGTGAAATAGCCGAGCGCCAACCAGCGCGTGGATTGCAAAAc < 1:894440/71‑1 (MQ=255)
gTAGAAAAATGCCGTAACTAAAAAAGTATGTGAAATAGCCGAGCGCCAACCAGCGCGTGGATTGCAAAAcc < 1:863597/71‑1 (MQ=255)
|
AACAGGCCGATGGTTTCTGGCGTTAAACCAATCCCTTTAAGCCAGACGCTCCAGAAAGGTAGAAAAATGCCGTAACTAAAAAAGTATGTGAAATAGCCGAGCGCCAACCAGCGCGTGGATTGCAAAACC > minE/1700402‑1700530
|
| 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
