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 |
|
A40 F1 I1 R1
|
16 |
59.7 |
3732628 |
97.2% |
3628114 |
76.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
3,875,632 |
(T)7→8 |
intergenic (‑66/+287) |
glmU ← / ← atpC |
bifunctional N‑acetylglucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyltransferase/F0F1 ATP synthase subunit epsilon |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 3,875,625 | 1 | . | T | 95.8%
| 186.2
/ 0.5
| 48 | intergenic (‑59/+294) | glmU/atpC | bifunctional N‑acetylglucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyltransferase/F0F1 ATP synthase subunit epsilon |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base T (25/21); total (25/23) |
| Fisher's exact test for biased strand distribution p-value = 2.24e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01 |
TAGCATTATTCAACATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑A‑TT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCGCTGACGAAAGCG > REL606/3875551‑3875693
|
tAGCATTATTCAACATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑A‑t < 1:912336/76‑1 (MQ=255)
aGCATTATTCAACATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑A‑tt > 1:1527059/1‑76 (MQ=255)
ttattCAACATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCANCTTGAAAAAACTAC‑A‑tt‑tttt > 2:301361/1‑76 (MQ=255)
ttattCAACATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑A‑tt‑tttt > 1:1140858/1‑76 (MQ=255)
ttattCAACATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑A‑tt‑tttt > 1:264020/1‑76 (MQ=255)
ttattCAACATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑A‑tt‑tttt > 1:1683538/1‑76 (MQ=255)
ttattCAACATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑A‑tt‑tttt < 2:1067751/76‑1 (MQ=255)
attCAACATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑A‑tt‑tttttt > 2:1635461/1‑75 (MQ=255)
ttCAACATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑A‑tt‑ttttttc < 1:216145/76‑3 (MQ=255)
aCATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCg < 1:1501286/76‑1 (MQ=255)
cATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGt < 1:1256/76‑1 (MQ=255)
aTACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTg < 1:136985/76‑1 (MQ=255)
aTACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTg < 2:225955/76‑1 (MQ=255)
aTACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTg < 1:1200584/76‑1 (MQ=255)
tACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGa > 2:668130/1‑76 (MQ=255)
gcgTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAAt < 2:831782/76‑1 (MQ=255)
cgTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATg > 2:181379/1‑76 (MQ=255)
cgTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATg > 1:499519/1‑76 (MQ=255)
tGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACag < 1:396072/76‑1 (MQ=255)
tGACTGTAATTTGAGAACAAATTAAACCCGCTTCACCTTAAAAAAACTACTT‑TT‑TTTTTCATCGTGAAATGGACag < 2:1029276/76‑1 (MQ=255)
aCTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACagag > 1:1688325/1‑76 (MQ=255)
aCTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACagag < 1:175268/76‑1 (MQ=255)
gTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGAt < 2:906453/76‑1 (MQ=255)
tAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATa < 1:1316789/76‑1 (MQ=255)
aTTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATaaa > 1:1246924/1‑76 (MQ=255)
ttGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAAtt > 1:398092/1‑76 (MQ=255)
gagaACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGt > 2:277553/1‑76 (MQ=255)
aCGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCaa > 2:745392/1‑76 (MQ=255)
cGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAAt > 1:1224445/1‑76 (MQ=255)
gAATTTAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATa < 1:28429/76‑1 (MQ=255)
gAATTTAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATa > 1:1442145/1‑76 (MQ=255)
aaTTTAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATaa < 1:671404/76‑1 (MQ=255)
ttAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACgg > 2:1845748/1‑76 (MQ=255)
ttAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACgg > 2:1764261/1‑76 (MQ=255)
ttAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACgg < 2:1558319/76‑1 (MQ=255)
tAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGa > 2:1110642/1‑76 (MQ=255)
tAAACCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGa > 2:696097/1‑76 (MQ=255)
aaaCCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGAt < 1:840132/76‑1 (MQ=255)
aCCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTa > 1:1540779/1‑76 (MQ=255)
aCCGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGAGCAGAGGATAAATTGTTCAATAACGGATTa < 2:71936/76‑1 (MQ=255)
ccGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTAt < 1:525379/76‑1 (MQ=255)
ccGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTAt < 1:345027/76‑1 (MQ=255)
ccGCTTCACCTTGAAAAAACTAC‑A‑TTGTTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTAt < 2:1306222/76‑1 (MQ=255)
cGCTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATc > 1:731672/1‑76 (MQ=255)
cTTCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATccc > 2:651941/1‑76 (MQ=255)
tCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCg > 2:1471886/1‑76 (MQ=255)
tCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCg < 2:704418/76‑1 (MQ=255)
tCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCg < 2:461654/76‑1 (MQ=255)
tCACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCg > 1:235035/1‑76 (MQ=255)
cACCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCGc > 1:1080495/1‑76 (MQ=255)
aCCTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCGCt > 2:866139/1‑76 (MQ=255)
ccTTGAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCGCTg > 1:832429/1‑76 (MQ=255)
gAAAAAACTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCGCTGACGa > 1:238012/1‑76 (MQ=255)
aaaaaaCTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCGCTGACGaa < 1:1281745/76‑1 (MQ=255)
aaaaaaCTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCGCTGACGaa < 2:220373/76‑1 (MQ=255)
aaaaCTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCGCTGACGAAAg > 2:880286/1‑76 (MQ=255)
aaCTAC‑ATTT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCGCTGACGAAAgcg > 1:1190979/1‑76 (MQ=255)
|
TAGCATTATTCAACATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTAC‑A‑TT‑TTTTTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCGCTGACGAAAGCG > REL606/3875551‑3875693
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
