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 |
|
A2 F8 I0 R2
|
296 |
77.6 |
4260404 |
88.1% |
3753415 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,789,346 |
Δ1 bp |
43.7% |
coding (483/1269 nt) |
ygaF → |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,789,346 | 0 | A | . | 43.7%
| 89.9
/ 111.2
| 64 | coding (483/1269 nt) | ygaF | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (15/21); new base . (18/10); total (33/31) |
| Fisher's exact test for biased strand distribution p-value = 8.41e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CCGTCCAGCGGCATTGTCAGCTACCGCGACGTGACGGCGGCGATGGCAAAAATCTTCCAGTCCAGAGGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATAAAAACGGCGTGGTGATACGTA > minE/1789281‑1789416
|
ccGTCCAGCGGCATTGTCAGCTACCGCGACGTGACGGCGGCGATGGCAAAAATCTTCCAGTCCAG‑GGCGGt > 1:1033040/1‑71 (MQ=255)
tCCAGCGGCATTGTCAGCTACCGCGACGTGACGCCGGCGATGGCAAAAATCTTCCAGTCCAGAGGCGGTGa < 1:4156667/71‑1 (MQ=255)
tCCAGCGGCATTGTCAGCTACCGCGACGCGACGGCGGCGATGGCAAAAATCTTCCAGTCCAG‑GGCGGTGa < 1:2964821/70‑1 (MQ=255)
cAGCGGCATTGTCAGCTACCGCGACGTGACGGCGGCGATGGCAAAAATCTTCCAGTCCAG‑GGCGGTGAAAt > 1:17475/1‑71 (MQ=255)
cAGCGGCATTGTCAGCTACCGCGACGTGACGGCGGCGATGGCAAAAATCTTCCAGTCCAG‑GGCGGTGAAAt > 1:1563971/1‑71 (MQ=255)
gCGGCATTGTCAGCTACCGCGACGTGACGGCGGCGATGGCAAAAATCTTCCAGTCCAGAGGCGGTGAAAtt < 1:1338213/71‑1 (MQ=255)
gCGGCATTGTCAGCTACCGCGACGTGACGGCGGCGATGGCAAAAATCTTCCAGTCCAGAGGCGGTGAAAt > 1:3876509/1‑70 (MQ=255)
gCATTGTCACCTACCGCGACGTGACGGCGGCGATGGCAAAAATCTTCCAGTCCAG‑GGCGGTGAAATTATc > 1:1189583/1‑70 (MQ=255)
cATTGTCAGCTACCGCGACGTGACGGCGGCGATGGCAAAAATCTTCCAGTCCAGAGGCGGTGAAATTATCt < 1:3557666/71‑1 (MQ=255)
aTTGTCAGCTACCGCGACGTGACGGCGGCGATGGCAAAAATCTTCCAGTCCAGAGGCGGTGAAATTATCt < 1:2137056/70‑1 (MQ=255)
aTTGTCAGCTACCGCGACGTGACGGCGGCGATGGCAAAAATCTTCCAGTCCAG‑GGCGGTGAAATTATCta > 1:2088390/1‑70 (MQ=255)
aTTGTCAGCTACCGCGACGTGACGGCGGCGATGGCAAAAATCTTCCAGTCCAG‑GGCGGTGAAATTATCta > 1:2313110/1‑70 (MQ=255)
aTTGTCAGCTACCGCGACGTGACGGCGGCGATGGCAAAAATCTTCCAGTCCAG‑GGCGGTGAAATTATCta > 1:2327360/1‑70 (MQ=255)
gTCAGCTACCGCGACGTGACGGCGGCGATGGCAAAAATCTTCCAGTCCAGAGGCGGTGAAAt > 1:1302927/1‑62 (MQ=255)
tACCGCGACGTGACGGCGGCGATGGCAAAAATCTTCCAGTCCAG‑GGCGGTGAAAt > 1:2618989/1‑55 (MQ=255)
gcgACGTGACGGCGGCGATGGCAAAAATCTTCCAGTCCAGAGGCGGTGAAATTATCTATAACGCCGAAGt > 1:389363/1‑70 (MQ=255)
gcgACGTGACGGCGGCGATGGCAAAAATCTTCCAGTCCAGAGGCGGTGAAATTATCTATAACGCCGAAGt > 1:3937176/1‑70 (MQ=255)
gcgACGTGACGGCGGCGATGGCAAAAATCTTCCAGTCCAGAGGCGGTGAAATTATCTATAACGCCGAAGt > 1:2123119/1‑70 (MQ=255)
cgACGTGACGGCGGCGATGGCAAAAATCTTCCAGTCCAG‑GGCGGTGAAATTATCTATAACGCCGAAGTCAg < 1:3107687/71‑1 (MQ=255)
cgACGTGACGGCGGCGATGGCAAAAATCTTCCAGTCCAG‑GGCGGTGAAATTATCTATAACGCCGAAGTCAg < 1:3672893/71‑1 (MQ=255)
ggcggcGATGGCAAAAATCTTCCAGTCCAGAGGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTa < 1:2964966/71‑1 (MQ=255)
ggcggcGATGGCAAAAATCTTCCAGTCCAG‑GGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTaa > 1:1421815/1‑71 (MQ=255)
ggcggcGATGGCAAAAATATTCCAGTCCAG‑GGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTaa > 1:3153320/1‑71 (MQ=255)
ggcgATGGCAAAAATCTTCCAGTCCAGAGGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATg < 1:2721975/71‑1 (MQ=255)
cgATGGCAAAAATCTTCCAGTCCAGAGGCGGTGAAATTATCtat < 1:3830524/44‑1 (MQ=255)
cgATGGCAAAAATCTTCCAGTCCAGAGGCGGTGAAATTATCtat < 1:3835515/44‑1 (MQ=255)
cgATGGCAAAAATCTTCCAGTCCAGAGGCGGTGAAATTATCtat < 1:229203/44‑1 (MQ=255)
cgATGGCAAAAATCTTCCAGTCCAGAGGCGGTGAAATTATCtat < 1:1397351/44‑1 (MQ=255)
aTGGCAAAAATCTTCCAGTCCAGAGGCGGTGAAATTATCTATAACGCCGaa > 1:2123177/1‑51 (MQ=255)
aTGGCAAAAATCTTCCAGTCCAGAGGCGGTGAAATTATCTATAACGCCGaa > 1:1214003/1‑51 (MQ=255)
aTGGCAAAAATCTTCCAGTCCAGAGGCGGTGAAATTATCTATAACGCCGaa > 1:1098148/1‑51 (MQ=255)
aTGGCAAAAATCTTCCAGTCCAGAGGCGGTGAAATTATCTATAACGCCGAAGTc < 1:2630632/54‑1 (MQ=255)
tGGCAAAAATCTTCCAGTCCAGAGGCTGTGAAATTATCTATAACGCCGAAGTGAGCGGGCTTa < 1:2226607/63‑1 (MQ=255)
tGGCAAAAATCTTCCAGTCCAG‑GGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTaa > 1:811352/1‑63 (MQ=255)
ggCAAAAATCTTCCAGTCCAG‑GGCGGTGAAATTATCTATAACGCCg > 1:3694510/1‑46 (MQ=39)
ggCAAAAATCTTCCAGTCCAG‑GGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATa > 1:1158030/1‑70 (MQ=255)
ggCAAAAATCTTCCAGTCCAG‑GGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATa > 1:1492321/1‑70 (MQ=255)
ggCAAAAATCTTCCAGTCCAG‑GGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATa > 1:2038708/1‑70 (MQ=255)
gCAAAAATCTTCCAGTCCAGAGGCGGTGAAATTATCTATaa > 1:674471/1‑41 (MQ=255)
gCAAAAATCTTCCAGTCCAGAGGCGGTGAAATTATCTATaa > 1:56326/1‑41 (MQ=255)
gCAAAAATCTTCCAGTCCAGAGGCGGTGAAATTATCTATaa > 1:2933145/1‑41 (MQ=255)
gCAAAAATCTTCCAGTCCAGAGGCGGTGAAATTATCTATAACGCCGAAGTc < 1:2604287/51‑1 (MQ=255)
gCAAAAATCTTCCAGTCCAG‑GGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATaaa < 1:2096370/71‑1 (MQ=255)
gCAAAAATCTTCCAGTCCAG‑GGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATaaa < 1:551636/71‑1 (MQ=255)
gCAAAAATCTTCCAGTCCAG‑GGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATaaa < 1:2129346/71‑1 (MQ=255)
cAAAAATCTTCCAGTCCAG‑GGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATaaaa < 1:1927418/71‑1 (MQ=255)
aaaaaTCTTCCAGTCCAGAGGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATaaaa < 1:1723147/71‑1 (MQ=255)
aaaaaTCTTCCAGTCCAGAGGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATaaaa < 1:1496582/71‑1 (MQ=255)
aaaaTCTTCCAGTCCAG‑GGCGGTGAAATTATCTATAACGCCGAAg < 1:2596965/45‑1 (MQ=39)
aaaaTCTTCCAGTCCAG‑GGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATaaa < 1:3399322/68‑1 (MQ=255)
aaaaTCTTCCAGTCCAG‑GGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATaaa < 1:55365/68‑1 (MQ=255)
tCTTCCAGTCCAGAGGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATAAAAACGGc > 1:2657484/1‑71 (MQ=255)
tCTTCCAGTCCAG‑GGCGGTGAAATTATCTATAACGc > 1:698935/1‑36 (MQ=37)
tCTTCCAGTCCAG‑GGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATAAAAACGGCg > 1:2178787/1‑71 (MQ=255)
tCTTCCAGTCCAG‑GGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATAAAAACGGCg > 1:2735693/1‑71 (MQ=255)
ccagtccagAGGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATAAAAACGGc < 1:2610973/67‑1 (MQ=255)
ccagtccagAGGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATAAAAACGGc < 1:128724/67‑1 (MQ=255)
ccagtccagAGGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATAAAAACGGc < 1:1702490/67‑1 (MQ=255)
gtccagAGGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATaaa < 1:2073031/58‑1 (MQ=255)
tccagAGGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATAAAAACGGCGTGGTGAt < 1:3310720/71‑1 (MQ=255)
tccagAGGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATAAAAACGGCGTGGTGAt < 1:3315706/71‑1 (MQ=255)
cagAGGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATAAAAACGGCGTGGTGATAc > 1:1375825/1‑71 (MQ=255)
cagAGGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATAAAAACGGCGTGGTGATAc > 1:3667508/1‑71 (MQ=255)
cagAGGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATAAAAACGGCGTGGTGATAc > 1:3662501/1‑71 (MQ=255)
agGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATAAAAACGGCGTGGTGATACGTa < 1:2512772/71‑1 (MQ=255)
agGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATAAAAACGGCGTGGTGATACGTa < 1:3386814/71‑1 (MQ=255)
|
CCGTCCAGCGGCATTGTCAGCTACCGCGACGTGACGGCGGCGATGGCAAAAATCTTCCAGTCCAGAGGCGGTGAAATTATCTATAACGCCGAAGTCAGCGGGCTTAATGAGCATAAAAACGGCGTGGTGATACGTA > minE/1789281‑1789416
|
| 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
