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 |
|
A42 F1 I1 R1
|
17 |
53.4 |
3386926 |
97.4% |
3298865 |
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 | 97.6%
| 158.4
/ ‑2.7
| 41 | 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 . (0/1); new base T (22/18); total (22/19) |
| Fisher's exact test for biased strand distribution p-value = 4.63e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.74e-01 |
AGCATTATTCAACATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACA‑‑TTTTTTT‑CATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCGCTGACGAAAGCG > REL606/3875552‑3875693
|
aGCATTATTCAACATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACA‑‑tt > 1:57099/1‑76 (MQ=255)
cATTATTCAACATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACA‑‑tttt > 1:159838/1‑76 (MQ=255)
cATTATTCAACATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACA‑‑tttt < 1:1445459/76‑1 (MQ=255)
attattCAACATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACA‑‑ttttt < 2:557129/76‑1 (MQ=255)
attattCAACATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACA‑‑ttttt < 1:778240/76‑1 (MQ=255)
ttCAACATACGCGTCCTGACTGTAATTCGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACA‑‑ttttttttc > 2:140770/1‑74 (MQ=255)
aCATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCg < 2:1537340/76‑1 (MQ=255)
cATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGt > 1:39838/1‑76 (MQ=255)
cATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGt > 2:1484841/1‑76 (MQ=255)
aTACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTg < 1:1643901/76‑1 (MQ=255)
tACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGa > 2:532398/1‑76 (MQ=255)
aCGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGaa > 2:1691202/1‑76 (MQ=255)
aCGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGaa > 2:202224/1‑76 (MQ=255)
aCGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGaa > 1:923927/1‑76 (MQ=255)
aCGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGaa > 1:292406/1‑76 (MQ=255)
cgcgTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGaaa > 2:460475/1‑76 (MQ=255)
cgcgTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGaaa < 1:379681/76‑1 (MQ=255)
cgcgTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGaaa > 2:544281/1‑76 (MQ=255)
cgTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGAAATg < 1:497609/76‑1 (MQ=255)
cgTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGAAATg < 1:155304/76‑1 (MQ=255)
cgTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGAAATg > 1:1402502/1‑76 (MQ=255)
cgTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGAAATg < 2:315191/76‑1 (MQ=255)
cTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTAAAAAAACTACAT‑TTTTTTT‑CATCGTGAAATGGACa < 2:321767/76‑1 (MQ=255)
tGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGAAATGGACag < 1:1099614/76‑1 (MQ=255)
tAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGAAATGGACAGAGGATa < 2:1236127/76‑1 (MQ=255)
tAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGAAATGGACAGAGGATa > 2:201641/1‑76 (MQ=255)
tAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGAAATGGACAGAGGATa < 1:1201718/76‑1 (MQ=255)
aaTTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGAAATGGACAGAGGATaa < 2:1379401/76‑1 (MQ=255)
aTTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGAAATGGACAGAGGATaaa > 1:632705/1‑76 (MQ=255)
tttGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGAAATGGACAGAGGATAAAt < 1:938761/76‑1 (MQ=255)
agaACGAATTTAAACCGCTTCACCTTGAGAAAACTACAT‑TTTTTTT‑CATCGTGAAATGGACAGAGGATAAATTGtt < 2:1676990/76‑1 (MQ=255)
gAATTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGAAATGGACAGAGGATAAATTGTTCAATa > 1:398122/1‑76 (MQ=255)
aaTTTAAACCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGAAATGGACAGAGGATAAATTGTTCAATaa > 2:31112/1‑76 (MQ=255)
ttAAACCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGAAATGGACAGAGGATAAATTGTTCAATAACgg < 2:37862/76‑1 (MQ=255)
tAAACCGCTTCACCTTGAAAAAACTACATTTTTTTTT‑CATCGTGAAATGGAAAGAGGATAAATTGTTCAATAACgg > 1:1238073/1‑76 (MQ=255)
aaCCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGAtt > 1:1417715/1‑76 (MQ=255)
aCCGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTa < 2:1266920/76‑1 (MQ=255)
ccGCTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTAt > 2:94497/1‑76 (MQ=255)
cTTCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATccc > 1:1563913/1‑76 (MQ=255)
tCACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCg > 1:900879/1‑76 (MQ=255)
cACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCGc > 2:637945/1‑76 (MQ=255)
cACCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCAGc > 1:1082471/1‑76 (MQ=255)
aCCTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCGCt < 1:211316/76‑1 (MQ=255)
cTTGAAAAAACTACAT‑TTTTTTT‑CATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCGCTGa < 2:207435/76‑1 (MQ=255)
cTTGAAAAAACTACA‑‑TTTTTTNGCATAGTGAAATGGACTGAGGATAAATTGTTCAATAACGGATTATCCCCGCTGa < 2:272790/76‑1 (MQ=255)
gAAAAAACTACAT‑TTTTTTT‑CATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCGCTGACGa > 1:661056/1‑76 (MQ=255)
aaaaaCTACAT‑TTTTTTT‑CATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCGCTGACGaaa < 1:1035576/76‑1 (MQ=255)
aaCTACAT‑TTTTTTT‑CATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCGCTGCCGAAAgcg < 1:346446/76‑1 (MQ=255)
|
AGCATTATTCAACATACGCGTCCTGACTGTAATTTGAGAACGAATTTAAACCGCTTCACCTTGAAAAAACTACA‑‑TTTTTTT‑CATCGTGAAATGGACAGAGGATAAATTGTTCAATAACGGATTATCCCCGCTGACGAAAGCG > REL606/3875552‑3875693
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ 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
