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 F8 I0 R2
|
422 |
46.8 |
3726540 |
94.7% |
3529033 |
61.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,071,419:1 |
+A |
100% |
coding (331/1296 nt) |
glgC → |
glucose‑1‑phosphate adenylyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,071,419 | 1 | . | A | 90.0%
| 130.6
/ 11.5
| 50 | coding (331/1296 nt) | glgC | glucose‑1‑phosphate adenylyltransferase |
| Reads supporting (aligned to +/- strand): ref base . (5/0); new base A (29/16); total (34/16) |
| Fisher's exact test for biased strand distribution p-value = 1.63e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.61e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
GTCATTCTTCAATGAAGAAATGAACGAGTTTGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGG‑AAAACTGGTATCGCGGCACCGCAGATGCGGTCACCCAAAACCTCGACATTATCCGCCGTTATAAAGCG > W3110S.gb/4071352‑4071487
|
gTCATTCTTCAATGAAGAAATGAACGGGTTTGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGG‑a < 1:2583206/69‑1 (MQ=255)
gTCATTCTTCAATGAAGAAATGAACGAGTTTGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGG‑aaa < 1:605678/71‑1 (MQ=255)
gTCATTCTTCAATGAAGAAATGAACGAGTTTGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGG‑aaa < 1:351464/71‑1 (MQ=255)
gTCATTCTTCAATGAAGAAATGAACGAGTTTGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGG‑aaa < 1:2964512/71‑1 (MQ=255)
gTCATTCTTCAATGAAGAAATGAACGAGTTTGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGG‑a < 1:386236/69‑1 (MQ=255)
aTTCTTCAATGAAGAAATGAACGAGTTTGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGG‑AAAACt > 1:47332/1‑71 (MQ=255)
ttcttcAATGAAGAAATGAACGAGTTTGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGG‑aaaaact < 1:1596446/71‑4 (MQ=255)
cttcAATGAAGAAATGAACGAGTTTGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGG‑AAAACTgg > 1:3224830/1‑70 (MQ=255)
cAATGAAGAAATGAACGAGTTTGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGt < 1:3130129/69‑1 (MQ=255)
cAATGAAGAAATGAACGAGTTTGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGt < 1:348162/69‑1 (MQ=255)
aagaaATGAACGAGTTTGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGTATCGCgg > 1:2935867/1‑71 (MQ=255)
tGAACGAGTTTGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGG‑aaa < 1:1453123/51‑1 (MQ=255)
tGAACGAGTTTGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGG‑aaa < 1:2082924/51‑1 (MQ=255)
tGAACGAGTTTGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGG‑aaa < 1:2737153/51‑1 (MQ=255)
tGAACGAGTTTGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGG‑aaa < 1:1765839/51‑1 (MQ=255)
tGAACGAGTTTGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGG‑aaa < 1:1863452/51‑1 (MQ=255)
tGAACGAGTTTGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGG‑aaa < 1:3695574/51‑1 (MQ=255)
tGAACGAGTTTGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGG‑aaa < 1:241072/51‑1 (MQ=255)
gAACGAGTTTGTCGATCTGCTGCCAGCACAGCAGAGAATGAGAGGGG‑aaaaa > 1:2270599/1‑51 (MQ=255)
gAACGAGTTTGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCg > 1:3645433/1‑69 (MQ=255)
aaCGAGTTTGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCa < 1:2008359/70‑1 (MQ=255)
aaCGAGTTTGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGG‑aaaaa > 1:2954255/1‑50 (MQ=255)
aaCGAGTTTGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGG‑aaaaa > 1:519829/1‑50 (MQ=255)
aCGAGTTTGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCa < 1:1064493/69‑1 (MQ=255)
tttGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCa < 1:145501/64‑1 (MQ=255)
tGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGt > 1:1708786/1‑70 (MQ=255)
tGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGt > 1:1458869/1‑70 (MQ=255)
tGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGt > 1:327557/1‑70 (MQ=255)
tGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGt > 1:834050/1‑70 (MQ=255)
tGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGt > 1:1699105/1‑70 (MQ=255)
tGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGt > 1:191107/1‑70 (MQ=255)
tGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGt > 1:250624/1‑70 (MQ=255)
tGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGt > 1:818915/1‑70 (MQ=255)
tGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGt > 1:2145721/1‑70 (MQ=255)
tGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGt > 1:126250/1‑70 (MQ=255)
tGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGt < 1:1238090/70‑1 (MQ=255)
gTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGGAAAAACTTGTATCGCGGCACCGCAGATGCGGTc < 1:3508772/70‑1 (MQ=255)
tCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGt < 1:3098740/68‑1 (MQ=255)
ctgctgCCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCg > 1:901658/1‑61 (MQ=255)
ctgctgCCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCg > 1:2957039/1‑61 (MQ=255)
ctgctgCCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCg > 1:1459763/1‑61 (MQ=255)
ctgctgCCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGTCACCCaa > 1:3622083/1‑70 (MQ=255)
ctgctgCCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGTCACCCaa > 1:2770404/1‑70 (MQ=255)
ctgctgCCAGCACAGCAGAGAATGAAAGGGG‑aaaa > 1:1351466/1‑35 (MQ=255)
ctgcCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGTCACCCaaa < 1:724658/68‑1 (MQ=255)
ctgcCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGTCACCCaaa < 1:1957694/68‑1 (MQ=255)
ctgcCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGTCACCCaaa < 1:3175344/68‑1 (MQ=255)
ctgcCAGCACAGCAGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGTCACCCaaa < 1:2019892/68‑1 (MQ=255)
agcacagcaGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGa > 1:482140/1‑49 (MQ=38)
cacagcaGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGTCACCCAAAACCTCGACAt < 1:2136845/71‑1 (MQ=255)
acagcaGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGTCACCCAAAACCTCGACAtt < 1:1652865/71‑1 (MQ=255)
acagcaGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGTCACCCAAAACCTCGACAtt < 1:2034712/71‑1 (MQ=255)
acagcaGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGTCACCCAAAACCTCGACAt > 1:3275896/1‑70 (MQ=255)
acagcaGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGTCACCCAAAACCTCGACAt > 1:1441808/1‑70 (MQ=255)
acagcaGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGTCACCCAAAACCTCGACAt > 1:292340/1‑70 (MQ=255)
acagcaGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGTCACCCAAAACCTCGACAt > 1:2696032/1‑70 (MQ=255)
acagcaGAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGTCACCCAAAACCTCGACAt > 1:2053976/1‑70 (MQ=255)
cagcagAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGa > 1:154699/1‑45 (MQ=38)
cagcagAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGa > 1:3422896/1‑45 (MQ=38)
cagcagAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGa > 1:1952810/1‑45 (MQ=38)
cagcagAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGa > 1:2237801/1‑45 (MQ=38)
cagcagAGAATGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGTCACCCAAAACCTCGACAtt < 1:1177836/70‑1 (MQ=255)
tGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGTCAc > 1:3334554/1‑44 (MQ=37)
tGAAAGGGGAAAAACTGGTATCGCGGCACCGCAGATGCGGTCAc > 1:2610785/1‑44 (MQ=37)
aaaGGGG‑AAAACTGGTATCGCGGCACCGCAGATGCGGTCACCCAAAACCTCGACATTATCCGCCGTtata > 1:1937489/1‑70 (MQ=255)
aaaGGGG‑AAAACTGGTATCGCGGCACCGCAGATGCGGTCACCCAAAACCTCGACATTATCCGCCGTtata > 1:1356533/1‑70 (MQ=255)
aaaGGGG‑AAAACTGGTATCGCGGCACCGCAGATGCGGTCACCCAAAACCTCGACATTATCCGCCGTtata > 1:953084/1‑70 (MQ=255)
gg‑AAAACTGGTATCGCGGCACCGCAGATGCGGTCACCCAAAACCTCGACATTATCCGCCGTTATAAAGCg > 1:2314431/1‑70 (MQ=255)
gg‑AAAACTGGTATCGCGGCACCGCAGATGCGGTCACCCAAAACCTCGACATTATCCGCCGTTATAAAGCg > 1:1368193/1‑70 (MQ=255)
|
GTCATTCTTCAATGAAGAAATGAACGAGTTTGTCGATCTGCTGCCAGCACAGCAGAGAATGAAAGGGG‑AAAACTGGTATCGCGGCACCGCAGATGCGGTCACCCAAAACCTCGACATTATCCGCCGTTATAAAGCG > W3110S.gb/4071352‑4071487
|
| 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
