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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,111,795 |
T→C |
11.3% |
C147R (TGC→CGC) |
agaI → |
galactosamine‑6‑phosphate isomerase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,111,795 | 0 | T | C | 11.3%
| 163.8
/ 11.1
| 62 | C147R (TGC→CGC) | agaI | galactosamine‑6‑phosphate isomerase |
| Reads supporting (aligned to +/- strand): ref base T (27/28); new base C (2/5); total (29/33) |
| Fisher's exact test for biased strand distribution p-value = 4.32e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01 |
CGAAGAGATAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTGAACGAACCGGGAGAAAGCCTGCAACCGGC > minE/2111725‑2111862
|
cGAATAGATAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTAt < 1:640025/71‑1 (MQ=255)
cGAAGAGATAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTAt < 1:3882548/71‑1 (MQ=255)
cGAAGAGATAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTAt < 1:2980975/71‑1 (MQ=255)
aaGAGATAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGc < 1:1041542/71‑1 (MQ=255)
aaGAGATAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGc > 1:644557/1‑71 (MQ=255)
agagATAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCg > 1:3100691/1‑71 (MQ=255)
gaTAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTACGCGTtc < 1:708232/71‑1 (MQ=255)
aTAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTAt < 1:1466637/64‑1 (MQ=255)
aTAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTtct > 1:950270/1‑71 (MQ=255)
aaaTGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCg > 1:3153107/1‑71 (MQ=255)
aaaTGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCg > 1:778634/1‑71 (MQ=255)
aTGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTtctc > 1:2913287/1‑68 (MQ=255)
aTGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGa > 1:1673101/1‑71 (MQ=255)
gagaCAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGAtt > 1:715248/1‑71 (MQ=255)
agaCAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGAtt < 1:905300/70‑1 (MQ=255)
agaCAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGAtt < 1:3347643/70‑1 (MQ=255)
agaCAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGAtt < 1:1788043/70‑1 (MQ=255)
agaCAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTg < 1:3219755/71‑1 (MQ=255)
agaCAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTg > 1:3594332/1‑71 (MQ=255)
agaCAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTACGCGTTCTCGGAtt < 1:505161/70‑1 (MQ=255)
agaCAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGG‑‑TGGATTTATGCGTTCTCGGATTggg > 1:2239206/1‑71 (MQ=255)
aCAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTAt < 1:1375679/55‑1 (MQ=255)
aCAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTggg > 1:3587243/1‑71 (MQ=255)
gagTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGa > 1:1071999/1‑70 (MQ=255)
agTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGAtt < 1:2814109/64‑1 (MQ=255)
agTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGaa > 1:3009682/1‑70 (MQ=255)
gTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTACGCGTTCTCGGATTGGGGaaaa < 1:953016/71‑1 (MQ=255)
gAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACgg < 1:2276229/71‑1 (MQ=255)
gAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACg < 1:3205511/70‑1 (MQ=255)
aaCGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGaaaaa < 1:1256384/67‑1 (MQ=255)
aCGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACg > 1:1640393/1‑68 (MQ=255)
aCGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGt > 1:2271960/1‑70 (MQ=255)
aCGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGt > 1:846350/1‑70 (MQ=255)
cGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTgg > 1:3538899/1‑58 (MQ=255)
ggTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGa < 1:1093197/52‑1 (MQ=255)
gTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGaaaa < 1:1222740/61‑1 (MQ=255)
tAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCtt < 1:2441735/71‑1 (MQ=255)
tAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCtt < 1:2080414/71‑1 (MQ=255)
tAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTACGCGTTCTCGGATTGGGGAAAAACGGTCATCtt < 1:2251126/71‑1 (MQ=255)
aaCGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTAt > 1:2274456/1‑38 (MQ=255)
aaCGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTAt > 1:1094609/1‑38 (MQ=255)
aCGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTgg > 1:510844/1‑71 (MQ=255)
aCGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTg < 1:1807811/70‑1 (MQ=255)
aaCCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTtc < 1:1132688/40‑1 (MQ=255)
aaCCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCt > 1:1403750/1‑71 (MQ=255)
ccTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCAt < 1:424567/61‑1 (MQ=255)
ccTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTg > 1:1865114/1‑70 (MQ=255)
cTGATTGCGCGCAAAGGCGGTCTGGATTTACGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTgaa > 1:1467341/1‑71 (MQ=255)
gATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTgaac > 1:3910703/1‑70 (MQ=255)
aTTGCGCGCAAAGGCTGTCTGGATTTATGCGTTCTCGGAtt < 1:2939162/41‑1 (MQ=255)
gcgcgcAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTgaacgaac < 1:2349877/70‑1 (MQ=255)
gcgcAAAGGCGGTCTGGATTTATGCGTTCTCGTATTg < 1:1820068/37‑1 (MQ=255)
gcgcAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACgg > 1:2970056/1‑48 (MQ=255)
cAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTGAACGAACCgg > 1:3106429/1‑68 (MQ=255)
cAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTGAACGAACCGGgag < 1:293985/71‑1 (MQ=255)
cAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTGAACGAACCGGgag < 1:1440076/71‑1 (MQ=255)
aaaGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTGAACGAACCGGgaga < 1:1319711/71‑1 (MQ=255)
aaGGCGGTCTGGATTTATGCGTTCTCGGATTgggg < 1:953597/35‑1 (MQ=255)
aGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCt < 1:1232593/48‑1 (MQ=255)
ggCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATc < 1:3255008/46‑1 (MQ=255)
ggCGGTCTGGATTTACGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTGAACGAACCGGGAGAAAg < 1:3602637/71‑1 (MQ=255)
gCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTGAACGAACCGGGAGAAAGc < 1:912596/71‑1 (MQ=255)
tCTGGATTTATGCGTTCTCGGATTGGGGAAAAACg < 1:2235858/35‑1 (MQ=255)
cTGGATTTACGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTGAACGAACCGGGAGAAAGCCTGc > 1:3904547/1‑70 (MQ=255)
tGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTGAACGAACCGGGAGAAAGCCTGCaa > 1:1593727/1‑71 (MQ=255)
aTTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTGAACGAAcc < 1:3177171/52‑1 (MQ=255)
tttATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTGAACGAACCGGGAGAAAGCCTGCAACCgg > 1:3207800/1‑71 (MQ=255)
ttATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTGAACGCACCGGGAGAAAGCCTGCAACCGGc > 1:3918506/1‑71 (MQ=255)
tATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTgaacgaa > 1:733243/1‑47 (MQ=255)
|
CGAAGAGATAAATGAGACAGAGTGCGAACGGGTAACGAACCTGATTGCGCGCAAAGGCGGTCTGGATTTATGCGTTCTCGGATTGGGGAAAAACGGTCATCTTGGGCTGAACGAACCGGGAGAAAGCCTGCAACCGGC > minE/2111725‑2111862
|
| 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
