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 F21 I0 R1
|
476 |
35.3 |
2812105 |
96.7% |
2719305 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,204,990 |
T→C |
13.0% |
intergenic (‑78/‑129) |
ygiP ← / → ttdA |
predicted DNA‑binding transcriptional regulator/L‑tartrate dehydratase, alpha subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,204,990 | 0 | T | C | 13.0%
| 113.1
/ 10.4
| 46 | intergenic (‑78/‑129) | ygiP/ttdA | predicted DNA‑binding transcriptional regulator/L‑tartrate dehydratase, alpha subunit |
| Reads supporting (aligned to +/- strand): ref base T (22/18); new base C (3/3); total (25/21) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.43e-01 |
AGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACA > W3110S.gb/3204927‑3205058
|
aGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTAtt < 1:2722787/71‑1 (MQ=255)
aTAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGt > 1:1498333/1‑71 (MQ=255)
aaGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGtt > 1:2325852/1‑70 (MQ=255)
aGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTTCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGa < 1:2231439/71‑1 (MQ=255)
cgcAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGAtt < 1:933337/71‑1 (MQ=255)
tATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTAtt > 1:1595897/1‑52 (MQ=255)
tATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACg < 1:1482707/68‑1 (MQ=255)
tATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAAc > 1:2644090/1‑71 (MQ=255)
tATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAAc < 1:1722170/71‑1 (MQ=255)
tATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAAc > 1:2155104/1‑71 (MQ=255)
tttCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTg > 1:301782/1‑71 (MQ=255)
tttCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTg > 1:908238/1‑71 (MQ=255)
tttCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTg > 1:865628/1‑71 (MQ=255)
tttCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTg > 1:85865/1‑71 (MQ=255)
tttCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTg > 1:2406858/1‑71 (MQ=255)
tttCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTAATTCTTATTTTCGCGTTGATTCACGa > 1:2172173/1‑67 (MQ=255)
tCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGa > 1:368971/1‑58 (MQ=255)
tCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGt > 1:1206361/1‑70 (MQ=255)
tCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGt > 1:498811/1‑70 (MQ=255)
tCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGt > 1:2106707/1‑70 (MQ=255)
cGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGtt < 1:2048271/70‑1 (MQ=255)
ttGCCATTCCCTGCTCTGGCGCAATATTCATTCTT‑TTTTCGCGTTGATTCACg < 1:2556904/53‑1 (MQ=255)
gCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATAtt < 1:1876303/70‑1 (MQ=255)
gCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATAtt > 1:2196694/1‑70 (MQ=255)
cATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGa < 1:992920/44‑1 (MQ=255)
ttCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGAtt < 1:151/44‑1 (MQ=255)
cccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACat > 1:715062/1‑61 (MQ=255)
cccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGt > 1:868382/1‑70 (MQ=255)
cccTGCTCTGGCACAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTg > 1:290864/1‑71 (MQ=255)
cTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTa < 1:792721/52‑1 (MQ=255)
tGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGa < 1:1459520/44‑1 (MQ=255)
tGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACata > 1:67396/1‑59 (MQ=255)
tGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACata > 1:513704/1‑59 (MQ=255)
tGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGc > 1:2264017/1‑70 (MQ=255)
ctctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGtt < 1:874547/48‑1 (MQ=255)
ctctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGtt < 1:1865475/48‑1 (MQ=255)
tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCa > 1:1106331/1‑60 (MQ=255)
tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCa > 1:624985/1‑60 (MQ=255)
tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCaaa > 1:2267665/1‑70 (MQ=255)
gcgcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCaaaaaa < 1:1004652/69‑1 (MQ=255)
cAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATaa < 1:1440100/71‑1 (MQ=255)
cAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATaa < 1:1186781/71‑1 (MQ=255)
cAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATaa < 1:1984536/71‑1 (MQ=255)
cAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATaa < 1:1249220/71‑1 (MQ=255)
tatTCATTCTTATTTTCGCGTTGATTCACGAACTGtt < 1:460997/37‑1 (MQ=255)
tatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTa < 1:728548/42‑1 (MQ=255)
ttcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACgg > 1:1434849/1‑51 (MQ=255)
ttcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACgg > 1:1474040/1‑51 (MQ=255)
ttcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACg > 1:1544605/1‑50 (MQ=255)
ttcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCaaaa < 1:2017964/59‑1 (MQ=255)
ttcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATaa < 1:2512916/66‑1 (MQ=255)
ttcactcTTATTTTCGCGTTGATTCACGAACTGTTAATTACata > 1:1148734/1‑44 (MQ=255)
cattcTTATTTTCGCGTTGATTCACGAACTGTTaa > 1:2100847/1‑35 (MQ=255)
cattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACcaca > 1:1360981/1‑71 (MQ=255)
cattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACca > 1:1203051/1‑69 (MQ=255)
|
AGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACA > W3110S.gb/3204927‑3205058
|
| 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
