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 |
|
A3 F2 I1 R1
|
2892 |
75.3 |
5698161 |
66.1% |
3766484 |
59.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
Exported |
190,132 |
A→G |
21.0% |
K543K (AAA→AAG) |
ldcC → |
lysine decarboxylase 2, constitutive |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | Exported | 190,132 | 0 | A | G | 21.0%
| 105.9
/ 24.8
| 57 | K543K (AAA→AAG) | ldcC | lysine decarboxylase 2, constitutive |
| Reads supporting (aligned to +/- strand): ref base A (24/21); new base G (2/10); total (26/31) |
| Fisher's exact test for biased strand distribution p-value = 4.74e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GTGGGATCGTAGTAGAGAAAACCGGCCCTTATAACCTGCTGTTTCTCTTTAGTATTGGCATCGATAAAACCAAAGCAATGGGATTATTGCGTGGGTTGACGGAATTCAAACGCTCTTACGATCTCAACCTGCG > Exported/190065‑190197
|
atGGCATCGTTGTTGAGAAAACCGGTCCGTATAACCTGCTGTTCCTGTTCAGCATCGGTATCGATAAGAcc < 1:719281/70‑1 (MQ=255)
atGGCATCGTTGTTGAGAAAACCGGTCCGTATAACCTGCTGTTCCTGTTCAGCATCGGTATCGATAAGAcc < 1:4827765/70‑1 (MQ=255)
tGGCATCGTTGTTGAGAAAACCGGTCCGTATAACCTGCTGTTCCTGTTCAGCATCGGTATCGATAAGACCa < 1:1566860/71‑1 (MQ=255)
ggATCGTAGTAGAGAAAACCGGCCCTTATAACCTGCTGTTTCTCTTTAGTATTGGCATCGATAAAACCa > 1:2260222/1‑69 (MQ=255)
caTCGTTGTTGAGAAAACCGGTCCGTATAACCTGCTGTTCCTGTTCAGCATCGGTATCGATAAGACCAAAg < 1:2596964/70‑1 (MQ=255)
caTCGTTGTTGAGAAAACCGGTCCGTATAACCTGCTGTTCCTGTTCAGCATCGGTATCGATAAGACCAAAg < 1:5253021/70‑1 (MQ=255)
aTCGTTGTTGAGAAAACCGGTCCGTATAACCTGCTGTTCCTGTTCAGCATCGGTATCGATAAGACCAAAGc < 1:2341838/71‑1 (MQ=255)
tCGTAGTAGAGAAAACCGGCCCTTATAACCTGCTGTTTCTCTTTAGTATTGGCATCGATAAAACCAAAGCa < 1:1695552/71‑1 (MQ=255)
agagAAAACCGGCCCTTATAACCTGCTGTTTCTCTTTAGTATTGGCATCGATAAAACCAAAGCAATGGGat > 1:2420110/1‑71 (MQ=255)
gagaAAACCGGCCCTTATAACCTGCTGTTTCTCTTTAGTATTGGCATCGATaaa > 1:4133317/1‑54 (MQ=255)
gagaAAACCGGCCCTTATAACCTGCTGTTTCTCTTTAGTATTGGCATCGATAAAACCaaa > 1:2881683/1‑60 (MQ=255)
gagaAAACCGGCCCTTATAACCTGCTGTTTCTCTTTAGTATTGGCATCGATAAAACCaaa > 1:644475/1‑60 (MQ=255)
gagaAAACCGGCCCTTATAACCTGCTGTTTCTCTTTAGTATTGGCATCGATAAAACCAAAGCAATGGGatt < 1:2332978/71‑1 (MQ=255)
gaAAACCGGCCCTTATAACCTGCTGTTTCTCTTTAGTATTGGCATCGATAAAACCAAAGCaa < 1:314931/62‑1 (MQ=255)
aaaCCGGTCCGTATAACCTGCTGTTCCTGTTCAGCATCGGTATCGATAAGAc < 1:299019/52‑1 (MQ=255)
aaaCCGGCCCTTATAACCTGCTGTTTCTCTTTAGTATTGGCATCGATAAAACCAAAGCAATGGGATTATTg < 1:1636107/71‑1 (MQ=255)
aaCCGGTCCGTATAACCTGCTGTTCCTGTTCAGCATCGGTATCGATAAGACCAAAGCa > 1:3654314/1‑58 (MQ=255)
aCCGGTCCGTATAACCTGCTGTTCCTGTTCAGCATCGGTATCGATAAGACCAAAGCac > 1:4835337/1‑57 (MQ=255)
gCCCTTATAACCTGCTGTTTCTCTTTAGTATTGGCATCGATAAAACCAAAGCAATGGGatt < 1:4273272/61‑1 (MQ=255)
ccTTATAACCTGCTGTTTCTCTTTAGTATTGGCATCGATAAAACCAAAGCAATGGGATTATTGCGTGGGtt < 1:4242036/71‑1 (MQ=255)
ttATAACCTGCTGTTTCTCTTTAGTATTGGCATCGATAAAACCAAAGCAATGGGATTATTGCGt < 1:20500/64‑1 (MQ=255)
gtataACCTGCTTTTCCTGTTCAGCATCGGTATCGATAAGACCAAAGc < 1:2075650/47‑1 (MQ=255)
gtataACCTGCTGTTCCTGTTCAGCATCGGTATCGATAAGACCAAAGc < 1:3049035/47‑1 (MQ=255)
tataACCTGCTGTTCCTGTTCAGCATCGGTATCGATAAGACCAAAg < 1:1458781/46‑1 (MQ=255)
ataACCTGCTGTTTCTCTTTAGTATTGGCATCGATAAAACCa > 1:2140347/1‑42 (MQ=255)
ataACCTGCTGTTTCTCTTTAGTATTGGCATCGATAAAACCa > 1:3481190/1‑42 (MQ=255)
ataACCTGCTGTTTCTCTTTAGTATTGGCATCGATAAAACCAAAGCAATGGGATTATTGCGTGGGTTGACg > 1:3610225/1‑71 (MQ=255)
taACCTGCTGTTTCTCTTTAGTATTGGCATCGATAAAACCAAAGCAATGGGATTATTGCGTg < 1:1997495/62‑1 (MQ=255)
taACCTGCTGTTTCTCTTTAGTATTGGCATCGATAAAACCAAAGCAATGGGATTATTGCGTg < 1:5092900/62‑1 (MQ=255)
taACCTGCTGTTTCTCTTTAGTATTGGCATCGATAAAACCAAAGCAATGGGATTATTGCGTGGGTTGACg > 1:2552889/1‑70 (MQ=255)
taACCTGCTGTTTCTCTTTAGTATTGGCATCGATAAAACCAAAGCAATGGGATTATTGCGTGGGTTGACg > 1:2942458/1‑70 (MQ=255)
taACCTGCTGTTTCTCTTTAGTATTGGCATCGATAAAACCAAAGCAATGGGATTATTGCGTGGGTTGACg > 1:3220666/1‑70 (MQ=255)
aCCTGCTGTTTCTCTTTAGTATTGGCATCGATAAAACCAAAGCAATGGGATTATTGCGTGGGTTGACGGaa < 1:3546979/71‑1 (MQ=255)
ctgTTTCTCTTTAGTATTGGCATCGATAAAACCAAAGCAATGGGATTATTGCGTGGGTTGACGGAATTCa < 1:5396298/70‑1 (MQ=255)
ttCTCTTTAGTATTGGCATCGATAAAACCAAAGCAATGGGATTATTGCGTGGGTTGACGGAATTCAAACGc > 1:981195/1‑71 (MQ=255)
tctcTTTAGTATTGGCATCGATAAAACCAAAGCaa > 1:372864/1‑35 (MQ=255)
tctcTTTAGTATTGGCATCGATAAAACCAAAGCaa > 1:3939650/1‑35 (MQ=255)
ctctTTAGTATTGGCATCGATAAAACCAAAGCAATGGGATTATTGCg > 1:322455/1‑47 (MQ=255)
ctctTTAGTATTGGCATCGATAAAACCAAAGCAATGGGATTATTGCg > 1:1604306/1‑47 (MQ=255)
ctctTTAGTATTGGCATCGATAAAACCAAAGCAATGGGATTATTGCg > 1:1817460/1‑47 (MQ=255)
tttAGTATTGGCATCGATAAAACCAAAGCAATggg < 1:120045/35‑1 (MQ=255)
tttAGTATTGGCATCGATAAAACCAAAGCAATggg < 1:1209427/35‑1 (MQ=255)
tttAGTATTGGCATCGATAAAACCAAAGCAATGGGatta < 1:2476409/39‑1 (MQ=255)
tAGTATTGGCATCGATAAAACCAAAGCAATGGGATTATTGCGTGGGTTGACGGAATTCaaa > 1:4734619/1‑61 (MQ=255)
tAGTATTGGCATCGATAAAACCAAAGCAATGGGATTATTGCGTGGGTTGACGGAATTCaaa > 1:1430040/1‑61 (MQ=255)
tAGTATTGGCATCGATAAAACCAAAGCAATGGGATTATTGCGTGGGTTGACGGAATTCAAACGCTCtt < 1:1558282/68‑1 (MQ=255)
tATTGGCATCGATAAAACCAAAGCAATGGGATTATTGCGTgg < 1:133266/42‑1 (MQ=255)
ggCATCGATAAAACCAAAGCAATGGGATTATTGCGTGGGTTGACGGAATTCAAACGCTCTTACGATCTCa < 1:5076680/70‑1 (MQ=255)
ggCATCGATAAAACCAAAGCAATGGGATTATTGCGTGGGTTGACGGAATTCAAACGCTCTTACGATCTCa < 1:5461790/70‑1 (MQ=255)
gCATCGATAAAACCAAAGCAATGGGATTATTGCGTGGGt > 1:1944948/1‑39 (MQ=255)
gCATCGATAAAACCAAAGCAATGGGATTATTGCGTGGGt > 1:4853962/1‑39 (MQ=255)
gCATCGATAAAACCAAAGCAATGGGATTATTGCGTGGGt > 1:5681768/1‑39 (MQ=255)
tCGATAAAACCAAAGCAATGGGATTATTGCGTGGGTTGACGGAATTCAAACGCTCTTACGAtc < 1:2309044/63‑1 (MQ=255)
cGATAAAACCAAAGCAATGGGATTATTGCGTGGGtt < 1:3931816/36‑1 (MQ=255)
cGATAAAACCAAAGCAATGGGATTATTGCGTGGGtt < 1:3588341/36‑1 (MQ=255)
cGATAAAACCAAAGCAATGGGATTATTGCGTGGGTTGACGGAATTCaaa > 1:980310/1‑49 (MQ=255)
aTAAAACCAAAGCAATGGGATTATTGCGTGGGTTGa > 1:24046/1‑36 (MQ=255)
aTAAAACCAAAGCAATGGGATTATTGCGTGGGTTGACGGAATTCAAACGCTCTTACGATCTCAACCTGCg > 1:341865/1‑70 (MQ=255)
|
GTGGGATCGTAGTAGAGAAAACCGGCCCTTATAACCTGCTGTTTCTCTTTAGTATTGGCATCGATAAAACCAAAGCAATGGGATTATTGCGTGGGTTGACGGAATTCAAACGCTCTTACGATCTCAACCTGCG > Exported/190065‑190197
|
| 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
