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 |
|
A25 F1 I1 R1
|
14 |
46.3 |
3075166 |
96.7% |
2973685 |
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 | 92.9%
| 147.2
/ 4.4
| 42 | 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 . (1/2); new base T (25/14); total (26/16) |
| Fisher's exact test for biased strand distribution p-value = 5.47e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.68e-01 |
ATAGCATTATTCAACATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACA‑‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCGCTGACGAAAGC > REL606/3875550‑3875692
|
aTAGCATTATTCAACATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACa < 1:726933/76‑1 (MQ=255)
tAGCATTATTCAACGTACGCGGCCTGACTGTAATTTGAGAACGAATTTAAACCACTTCTCCTTGAAAAAACTACA‑‑t < 2:228290/76‑1 (MQ=255)
aGCATTATTCAACATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACA‑‑tt < 1:687967/76‑1 (MQ=255)
aCATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCg > 1:1149183/1‑76 (MQ=255)
tACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGa > 1:1077179/1‑76 (MQ=255)
aCGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGaa < 1:296354/76‑1 (MQ=255)
cgcgTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGaaa > 2:1415110/1‑76 (MQ=255)
cgcgTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACA‑‑TTT‑TAT‑TTCATCGTGaaa < 1:107752/76‑1 (MQ=255)
gcgTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTAATCGTGAAAt > 2:189363/1‑76 (MQ=255)
cTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACa < 2:1489044/76‑1 (MQ=255)
cTGACAGAAATTTGAAAAAAAATTAAAACCGCATCACCATAAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACa < 2:573877/76‑1 (MQ=255)
tGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACag < 2:1077925/76‑1 (MQ=255)
tGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACag < 2:1342386/76‑1 (MQ=255)
gACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACaga > 2:494512/1‑76 (MQ=255)
aCTGTAATTTGAGAACGAATTTAAACCGCTTCACATATAAAAAACTANAT‑TTT‑T‑T‑TTCATCGTGAAATGGACagag > 1:139740/1‑76 (MQ=255)
gTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGAt < 1:1299713/76‑1 (MQ=255)
aTTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATaaa < 1:343971/76‑1 (MQ=255)
ttGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAAtt > 2:1416736/1‑76 (MQ=255)
ttGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAAtt > 2:1416711/1‑76 (MQ=255)
gagaACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAATTGt > 1:1255996/1‑76 (MQ=255)
agaACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAATTGtt > 1:852426/1‑76 (MQ=255)
gaACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAATTGTTc > 1:786347/1‑76 (MQ=255)
aaCGAATTTAAACNGCTTCACCTTGAAAAATCTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAATTGTTCa < 2:1404489/76‑1 (MQ=255)
aaCGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAATTGTTCa < 1:656248/76‑1 (MQ=255)
aaTTTAGACCGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAATTGTTCAATaa < 1:1400138/76‑1 (MQ=255)
aaTTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAATTGTTCAATaa < 2:1341294/76‑1 (MQ=255)
tttAAACCGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACg > 1:524849/1‑76 (MQ=255)
tttAAACCGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACg < 1:1262400/76‑1 (MQ=255)
ttAAACCGCTTCACCTTGAAAAGACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAGTTGTTCAATAACgg > 2:239182/1‑76 (MQ=255)
tAAACCGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGa > 1:1498203/1‑76 (MQ=255)
tAAACCGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGa > 2:808699/1‑76 (MQ=255)
aaaCCGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGAt > 2:898322/1‑76 (MQ=255)
aaaCCGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGAt > 2:898339/1‑76 (MQ=255)
aaCCGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGAtt > 2:493453/1‑76 (MQ=255)
ccGCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTAt < 2:1088989/76‑1 (MQ=255)
gCTTCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATcc > 1:211636/1‑76 (MQ=255)
cTTCACCTTGAAAAAACTACA‑‑TTTAT‑T‑TACANCGTGAAATAGACAGNGGATANATTGTTCAATAACCGATTATccc < 2:206217/76‑1 (MQ=255)
ttCACCTTGAAAAAACTACA‑‑TTT‑T‑TCTTCATCGTGAAATGNNCAGAGGATAANNTATTCAATAACGGATTATcccc > 1:1383301/1‑76 (MQ=255)
tCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCg > 1:955084/1‑76 (MQ=255)
tCACCTTGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCg > 2:710650/1‑76 (MQ=255)
aCCTTGAAAAAACTACATTTTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCGc > 1:1264927/1‑76 (MQ=255)
ttGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCGCTGAc < 2:1149183/76‑1 (MQ=255)
ttGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCGCTGAc > 1:1334784/1‑76 (MQ=255)
tGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCGCTGACg > 1:840533/1‑76 (MQ=255)
tGAAAAAACTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCGCTGACg < 1:1180432/76‑1 (MQ=255)
aaaCTACAT‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCGCTGACGAAAgc > 2:1014679/1‑76 (MQ=255)
|
ATAGCATTATTCAACATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACA‑‑TTT‑T‑T‑TTCATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCGCTGACGAAAGC > REL606/3875550‑3875692
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
