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 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
871,945 |
C→T |
26.3% |
G648G (GGC→GGT) |
topA → |
DNA topoisomerase I, omega subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 871,945 | 0 | C | T | 26.3%
| 59.3
/ 17.6
| 53 | G648G (GGC→GGT) | topA | DNA topoisomerase I, omega subunit |
| Reads supporting (aligned to +/- strand): ref base C (18/21); new base T (11/3); total (29/24) |
| Fisher's exact test for biased strand distribution p-value = 5.95e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01 |
AAAGAGCGTTGCAAAACCACCATTAACCTGGTGCCGGAAAACGAAGTGCTGAACGTGCTGGAAGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAACGTCGTTGCCCGAAATGCGGCACGGCGATG > minE/871880‑872008
|
aaaGAGCGTTGCAAAACCACCATTAACCTGGTGCCGGAAAACGAAGTGCTGAACGTGCTGGAAGGCGaa < 1:2554781/69‑1 (MQ=255)
aaaGAGCGTTGCAAAACCACCATTAACCTGGTGCCGGAAAACGAAGTGCTGAACGTGCTGGAAGGCGaa < 1:529694/69‑1 (MQ=255)
tGCAAAACCACCATTAACCTGGTGCCGGAAAACGAAGTGCTGAACGTGCTGGAAGGTGAAGACGCt > 1:1767471/1‑66 (MQ=255)
tGCAAAACCACCATTAACCTGGTGCCGGAAAACGAAGTGCTGAACGTGCTGGAAGGTGAAGACGCTGaa > 1:1699143/1‑69 (MQ=255)
tGCAAAACCACCATTAACCTGGTGCCGGAAAACGAAGTGCTGAACGTGCTGGAAGGTGAAGACGCTGaa > 1:3028022/1‑69 (MQ=255)
tGCAAAACCACCATTAACCTGGTGCCGGAAAACGAAGTGCTGAACGTGCTGGAAGGTGAAGACGCTGaa > 1:3113/1‑69 (MQ=255)
tGCAAAACCACCATTAACCTGGTGCCGGAAAACGAAGTGCTGAACGTGCTGGAAGGTGAAGACGCTGaa > 1:3275707/1‑69 (MQ=255)
tGCAAAACCACCATTAACCTGGTGCCGGAAAACGAAGTGCTGAACGTGCTGGAAGGTGAAGACGCTGaa > 1:404945/1‑69 (MQ=255)
tGCAAAACCACCATTAACCTGGTGCCGGAAAACGAAGTGCTGAACGTGCTGGAAGGTGAAGACGCTGaa > 1:174647/1‑69 (MQ=255)
tGCAAAACCACCATTAACCTGGTGCCGGAAAACGAAGTGCTGAACGTGCTGGAAGGTGAAGACGCTGaa > 1:1531695/1‑69 (MQ=255)
tGCAAAACCACCATTAACCTGGTGCCGGAAAACGAAGTGCTGAACGTGCTGGAAGGTGAAGACGCTGaa > 1:1492473/1‑69 (MQ=255)
tGCAAAACCACCATTAACCTGGTGCCGGAAAACGAAGTGCTGAACGTGCTGGAAGGTGAAGACGCTGaa > 1:900650/1‑69 (MQ=255)
tGCAAAACCACCATTAACCTGGTGCCGGAAAACGAAGTGCTGAACGTGCTGGAAGGTGAAGACGCTGaa > 1:1022422/1‑69 (MQ=255)
aTTAACCTGGTGCCGGAAAACGAAGTGCTGAACGTGCTGGAAGGCGaa > 1:504034/1‑48 (MQ=255)
aTTAACCTGGTGCCGGAAAACGAAGTGCTGAACGTGCTGGAAGGCGaa > 1:1409879/1‑48 (MQ=255)
aTTAACCTGGTGCCGGAAAACGAAGTGCTGAACGTGCTGGAAGGCGaa > 1:3271862/1‑48 (MQ=255)
aTTAACCTGGTGCCGGAAAACGAAGTGCTGAACGTGCTGGAAGGCGaa > 1:1076489/1‑48 (MQ=255)
aaCCTGGTGCCGGAAAACGAAGTGCTGAACGTGCTGGAAGGTGAAGACGCTGaa < 1:1798144/54‑1 (MQ=38)
aaCCTGGTGCCGGAAAACGAAGTGCTGAACGTGCTGGAAGGTGAAGACGCTGaa < 1:2288071/54‑1 (MQ=38)
aaCCTGGTGCCGGAAAACGAAGTGCTGAACGTGCTGGAAGGTGAAGACGCTGaa < 1:3011716/54‑1 (MQ=38)
gCCGGAAAACGAAGTGCTGAACGTGCTGGAAGGCGAAGATGCTGAAGCCAACGCGCTGCGCGCAAAAcg > 1:169946/1‑69 (MQ=255)
aaaCGAAGTGCTGAACGTGCTGGAAGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAACGTCGtt > 1:3308221/1‑68 (MQ=255)
aaaCGAAGTGCTGAACGTGCTGGAAGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAACGTCGTTg > 1:972674/1‑69 (MQ=255)
aaaCGAAGTGCTGAACGTGCTGGAAGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAACGTCGTTg > 1:777440/1‑69 (MQ=255)
aaaCGAAGTGCTGAACGTGCTGGAAGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAACGTCGTTg > 1:822966/1‑69 (MQ=255)
aaaCGAAGTGCTGAACGTGCTGGAAGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAACGTCGTTg > 1:938815/1‑69 (MQ=255)
aaaCGAAGTGCTGAACGTGCTGGAAGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAACGTCGTTg > 1:1009836/1‑69 (MQ=255)
aaaCGAAGTGCTGAACGTGCTGGAAGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAACGTCGTTg > 1:2508191/1‑69 (MQ=255)
aaaCGAAGTGCTGAACGTGCTGGAAGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAACGTCGTTg > 1:1364258/1‑69 (MQ=255)
aaaCGAAGTGCTGAACGTGCTGGAAGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAACGTCGTTg > 1:2320771/1‑69 (MQ=255)
aaaCGAAGTGCTGAACGTGCTGGAAGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAACGTCGTTg > 1:2238051/1‑69 (MQ=255)
aaGTGCTGAACGTGCTGGAAGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAAcgt < 1:2628805/59‑1 (MQ=255)
aaGTGCTGAACGTGCTGGAAGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAAcgt < 1:118355/59‑1 (MQ=255)
aaGTGCTGAACGTGCTGGAAGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAAcgt < 1:87375/59‑1 (MQ=255)
aaGTGCTGAACGTGCTGGAAGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAAcgt < 1:1395157/59‑1 (MQ=255)
aaGTGCTGAACGTGCTGGAAGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAAcgt < 1:523288/59‑1 (MQ=255)
aaGTGCTGAACGTGCTGGAAGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAAcgt < 1:1477900/59‑1 (MQ=255)
aaGTGCTGAACGTGCTGGAAGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAAcgt < 1:444225/59‑1 (MQ=255)
aaGTGCTGAACGTGCTGGAAGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAAcgt < 1:41472/59‑1 (MQ=255)
aaGTGCTGAACGTGCTGGAAGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAAcgt < 1:3420791/59‑1 (MQ=255)
gAACGTGCTGGAAGGCGAAGATTCTGAAACCAACGCGCTGCGCGCAAAACGTCGTTGCCCGAAATGCgg > 1:1941146/1‑69 (MQ=255)
gAACGTGCTGGAAGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAACGTCGTTGCCCGAAATGCgg > 1:263300/1‑69 (MQ=255)
gAACGTGCTGGAAGGCAAAGATGCTGAAACCAACGCGCTGCGCGCAAAACGTCGTTGCCCGAAATGCgg > 1:228978/1‑69 (MQ=255)
tGCTGGAAGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAAcgt < 1:1291616/47‑1 (MQ=255)
aGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAACGTCGTTGCCCGAAATGCGGCACGGCGATg < 1:1803693/67‑1 (MQ=255)
aGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAACGTCGTTGCCCGAAATGCGGCACGGCGATg < 1:42285/67‑1 (MQ=255)
aGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAACGTCGTTGCCCGAAATGCGGCACGGCGATg < 1:1967599/67‑1 (MQ=255)
aGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAACGTCGTTGCCCGAAATGCGGCACGGCGATg < 1:1425294/67‑1 (MQ=255)
aGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAACGTCGTTGCCCGAAATGCGGCACGGCGATg < 1:678550/67‑1 (MQ=255)
aGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAACGTCGTTGCCCGAAATGCGGCACGGCGATg < 1:2369427/67‑1 (MQ=255)
aGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAACGTCGTTGCCCGAAATGCGGCACGGCGATg < 1:2748421/67‑1 (MQ=255)
aGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAACGTCGTTGCCCGAAATGCGGCACGGCGATg < 1:1284992/67‑1 (MQ=255)
aGGCGAAGATGCTGAAACCAACGCGCTGCACGCAAAACGTCGTTGCCCGAAATGCGGCACGGCGATg < 1:520340/67‑1 (MQ=255)
|
AAAGAGCGTTGCAAAACCACCATTAACCTGGTGCCGGAAAACGAAGTGCTGAACGTGCTGGAAGGCGAAGATGCTGAAACCAACGCGCTGCGCGCAAAACGTCGTTGCCCGAAATGCGGCACGGCGATG > minE/871880‑872008
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
