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 R1
|
311 |
50.1 |
4085234 |
95.9% |
3917739 |
60.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,508,088 |
C→A |
30.1% |
G615V (GGC→GTC) |
ypdD ← |
fused predicted PTS enzymes Hpr component, enzyme I component, and enzyme IIA component |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,508,088 | 0 | C | A | 30.1%
| 115.3
/ 27.1
| 56 | G615V (GGC→GTC) | ypdD | fused predicted PTS enzymes Hpr component, enzyme I component, and enzyme IIA component |
| Reads supporting (aligned to +/- strand): ref base C (27/12); new base A (9/8); total (36/20) |
| Fisher's exact test for biased strand distribution p-value = 3.63e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCTACTCATACTCAGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTATTTGCTGCAACAT > W3110S.gb/2508024‑2508155
|
gCTACTCATACTCAGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAGtt < 1:2918506/71‑1 (MQ=255)
ctcatactcaGCTCATCAAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAGTTCAc > 1:3683969/1‑70 (MQ=255)
catactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGTCAGATAACGGCTTTCACCGCCCAGTTCACCg > 1:2361267/1‑70 (MQ=255)
catactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCg > 1:3658990/1‑70 (MQ=255)
catactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCg > 1:2878805/1‑70 (MQ=255)
catactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAGTTCACCg > 1:1410778/1‑70 (MQ=255)
atactcaGCTCATCCAGGCCCCGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCg > 1:4022678/1‑69 (MQ=255)
atactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCa < 1:2246787/71‑1 (MQ=255)
atactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAGTTCACCGc > 1:1391905/1‑70 (MQ=255)
atactcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAGTTCACCGCa < 1:2759365/71‑1 (MQ=255)
atacacaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGCCAGATAACGGCTTTCACCGCCCAGTACACCGc > 1:4027492/1‑70 (MQ=255)
ctcaGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAGTTCACCGCAAAt > 1:417976/1‑71 (MQ=255)
tCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAAt < 1:402606/65‑1 (MQ=255)
tCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAAt < 1:2144989/65‑1 (MQ=255)
tCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAAt < 1:1301885/65‑1 (MQ=255)
tCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTAc > 1:746835/1‑71 (MQ=255)
aTCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGc > 1:1989443/1‑65 (MQ=255)
aTCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAGTTCACCGCAAATGc > 1:2792414/1‑65 (MQ=255)
aTCCAGGCCCAGCCCAAGAAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACAGCAAATGc > 1:2139302/1‑65 (MQ=255)
tCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCa < 1:2214410/71‑1 (MQ=255)
tCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAGTTCACCGct < 1:383877/59‑2 (MQ=255)
tCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAGTTCACCGCa < 1:1733523/59‑1 (MQ=255)
tCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAGTTCACCGCa < 1:728876/59‑1 (MQ=255)
ccAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGACCAGTTCACCGCAAATGCCTa > 1:2562335/1‑66 (MQ=255)
cAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGc > 1:3195710/1‑44 (MQ=255)
cAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGc > 1:936881/1‑44 (MQ=255)
cAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGc > 1:4023420/1‑44 (MQ=255)
cAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGt > 1:1929665/1‑49 (MQ=255)
cAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCa > 1:371867/1‑57 (MQ=255)
cAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCAtt > 1:1227555/1‑71 (MQ=255)
cagcgcaAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCa > 1:3330839/1‑51 (MQ=255)
cagcccaAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGc > 1:134982/1‑50 (MQ=255)
cagccaaAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCa > 1:2346118/1‑51 (MQ=255)
cccaAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCt < 1:2100628/71‑1 (MQ=255)
cccaAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCt < 1:3729279/71‑1 (MQ=255)
cccaAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCt < 1:2201267/71‑1 (MQ=255)
cAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATgcg < 1:393220/71‑1 (MQ=255)
gTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATgcg > 1:1894357/1‑69 (MQ=255)
aGCGGCAGATAACGGCTTTCACCGACCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGt > 1:2531135/1‑71 (MQ=255)
gCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTg > 1:3200407/1‑71 (MQ=255)
aGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTAc > 1:663519/1‑41 (MQ=255)
aGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAAc > 1:2276625/1‑71 (MQ=255)
gATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCt < 1:353486/38‑1 (MQ=255)
aTAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTa < 1:3437265/71‑1 (MQ=255)
tAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTaa > 1:1673255/1‑67 (MQ=255)
tAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTaa > 1:132011/1‑67 (MQ=255)
aaCGGCTTTCACCGACCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATgcgc > 1:2145587/1‑58 (MQ=255)
aaCGGCTTTCACCGACCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAg > 1:717102/1‑60 (MQ=255)
cGGCTTTCACCGACCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCt < 1:2285095/49‑1 (MQ=255)
ggCTTTCACCGACCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCt < 1:849256/48‑1 (MQ=255)
tttCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGt > 1:3830544/1‑55 (MQ=255)
tttCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGt > 1:2185222/1‑55 (MQ=255)
tttCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGt > 1:2692938/1‑55 (MQ=255)
tttCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTATTtgctg > 1:4014023/1‑70 (MQ=255)
tttCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTATTtgctg > 1:218941/1‑70 (MQ=255)
tttCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTATTtgctg > 1:129841/1‑70 (MQ=255)
cACCGACCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTATTTGCTGCaa < 1:2371754/70‑1 (MQ=255)
aCCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTATTTGCTGCAACa > 1:791426/1‑71 (MQ=255)
ccGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTATTTGCTGCAACAt < 1:3870632/71‑1 (MQ=255)
|
GCTACTCATACTCAGCTCATCCAGGCCCAGCCCAAGCAGTAGCGGCAGATAACGGCTTTCACCGCCCAGTTCACCGCAAATGCCTACCCATTTGCCCCGCTGATGCGCAGTGGTAACTATTTGCTGCAACAT > W3110S.gb/2508024‑2508155
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
