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 F1 I0 R1
|
2892 |
75.3 |
5698161 |
66.1% |
3766484 |
59.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,019,201 |
G→A |
55.4% |
intergenic (+150/+76) |
ydgA → / ← uidC |
conserved hypothetical protein/predicted outer membrane porin protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,019,201 | 0 | G | A | 55.4%
| 27.1
/ 87.4
| 74 | intergenic (+150/+76) | ydgA/uidC | conserved hypothetical protein/predicted outer membrane porin protein |
| Reads supporting (aligned to +/- strand): ref base G (14/19); new base A (19/22); total (33/41) |
| Fisher's exact test for biased strand distribution p-value = 8.16e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.14e-01 |
CAGGCCTACCTTTTCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCACTTTGTCAACAATCTGAAACGCCGGAGATTTTTCTC > minE/1019136‑1019262
|
cAGGCCTACCTTTTCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCa > 1:1883038/1‑71 (MQ=255)
aGGCCTACCTTTTCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCa < 1:3862038/70‑1 (MQ=255)
ggCCTACCTTTTCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATc < 1:375461/71‑1 (MQ=255)
ggCCTACCTTTTCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATc < 1:2845017/71‑1 (MQ=255)
ctatgcctgatgcgacgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATc < 1:4228679‑M2/14‑1 (MQ=255)
ctatgcctgatgcgacgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATc < 1:1437379‑M2/14‑1 (MQ=255)
tatgcctgatgcgacgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATcc > 1:2101907‑M2/57‑71 (MQ=255)
tatgcctgatgcgacgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATcc > 1:1903227‑M2/57‑71 (MQ=255)
tatgcctgatgcgacgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATcc > 1:1004805‑M2/57‑71 (MQ=255)
atgcctgatgcgacgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATc > 1:1415165‑M2/56‑69 (MQ=255)
atgcctgatgcgacgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATc > 1:2946535‑M2/56‑69 (MQ=255)
cTACCTTTTCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCgg > 1:2754390/1‑71 (MQ=255)
tACCTTTTCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTAcgtcgc < 1:4775957/64‑1 (MQ=255)
tACCTTTTCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTAcgccgc < 1:3032851/64‑1 (MQ=255)
aCCTTTTCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCa > 1:4171515/1‑71 (MQ=255)
cTTTTCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATa < 1:2408845/71‑1 (MQ=255)
gatgcgacgctgaagcgtcttatcaagcctacatagcactgccacgtatGTTTACACCGCATCCGGCATa > 1:818729‑M2/50‑70 (MQ=255)
atgcgacgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATaa < 1:713490‑M2/22‑1 (MQ=255)
tgcgacgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATaa < 1:2048094‑M2/22‑1 (MQ=255)
tgcgacgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATaa < 1:2484138‑M2/22‑1 (MQ=255)
tgcgacgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATaa < 1:4048171‑M2/22‑1 (MQ=255)
tCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATaaaa < 1:1845442/70‑1 (MQ=255)
cgacgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCAtaaaaac < 1:274881‑M2/26‑2 (MQ=255)
ccTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATaaaa < 1:4027220/69‑1 (MQ=255)
gacgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCataaaaaca > 1:1857692‑M2/45‑69 (MQ=255)
cTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑Ac < 1:5511288/71‑1 (MQ=255)
cTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑Ac < 1:1111320/71‑1 (MQ=255)
acgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGcataaaaacac < 1:2096420‑M2/28‑4 (MQ=255)
acgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATaaaaa < 1:3098024‑M2/25‑1 (MQ=255)
acgctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATaaaaa < 1:1281470‑M2/25‑1 (MQ=255)
ctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATaaa < 1:1279892‑M2/23‑1 (MQ=255)
ctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATaaa < 1:2391419‑M2/23‑1 (MQ=255)
ctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATAAAAACAcgcg < 1:3770558‑M2/31‑1 (MQ=255)
ctgaagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATAAAAACAcgcg < 1:4858968‑M2/31‑1 (MQ=255)
acacTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCa > 1:1026075/1‑71 (MQ=255)
cacTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCAc < 1:829182/71‑1 (MQ=255)
aagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATAAAAACACGCGCa < 1:4692444‑M2/33‑1 (MQ=255)
aagcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATAAAAACACGCGCAc > 1:774384‑M2/38‑71 (MQ=255)
cTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCa < 1:1365159/48‑1 (MQ=255)
cTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCa < 1:4097776/48‑1 (MQ=255)
agcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATAAAAACACGCGCAc < 1:3150977‑M2/34‑1 (MQ=255)
tttGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCACttt > 1:3941050/1‑71 (MQ=255)
gcgtcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATAAAAACACGCGCACtt > 1:1562269‑M2/36‑71 (MQ=255)
ttGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCa > 1:2617432/1‑46 (MQ=255)
tGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATaaaa < 1:3349831/57‑1 (MQ=255)
tGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCACTTTg < 1:1034573/70‑1 (MQ=255)
tcttatcatgcctacatagcactgccacgtatGTTTTCACCGCATCCGGCAtat < 1:208239‑M2/22‑2 (MQ=255)
tcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATaaa < 1:5660959‑M2/23‑1 (MQ=255)
tcttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATaaa < 1:1078565‑M2/23‑1 (MQ=255)
cttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATAAAAACACGCGCACTTTg > 1:4855398‑M2/32‑69 (MQ=255)
ttatcatgcctacatagcactgccacgtatGTTTACACCGCATCCGGCATAAAAACACGCGCACtttgcta > 1:5651377‑M2/31‑68 (MQ=255)
tATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCACTTTGTcaacaa > 1:4326407/1‑71 (MQ=255)
aGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCACtt < 1:687423/58‑1 (MQ=255)
aGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCACTTTGTCAACAATCt > 1:5362425/1‑70 (MQ=255)
gTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCACTTTGTCAACAATCTGa < 1:5690720/71‑1 (MQ=255)
tttttGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCACTTTg < 1:3932357/58‑1 (MQ=255)
catagcactgcaacgtatGTTTACACCGCATCCGGCataaaaaca > 1:194876‑M2/19‑43 (MQ=255)
atagcactgccacgtatGTTTACACCGCATCCGGCATaaa < 1:5174100‑M2/23‑1 (MQ=255)
atagcactgccacgtatGTTTACACCGCATCCGGCATaaa < 1:1356576‑M2/23‑1 (MQ=255)
tagcactgccacgtatGTTTACACCGCATCCGGCATaaaaa > 1:4103816‑M2/17‑41 (MQ=255)
agcactgccacgtatGTTTACACCGCATCCGGCATaaaaa > 1:781077‑M2/16‑40 (MQ=255)
agcactgccacgtatGTTTACACCGCATCCGGCATaaaaa > 1:1438687‑M2/16‑40 (MQ=255)
agcactgccacgtatGTTTACACCGCATCCGGCATaaaaa > 1:1712395‑M2/16‑40 (MQ=255)
agcactgccacgtatGTTTACACCGCATCCGGCATaaaaa > 1:462448‑M2/16‑40 (MQ=255)
gcactgccacgtatGTTTACACCGCATCCGGCataaaaaca > 1:2988740‑M2/15‑39 (MQ=255)
gcactgccacgtatGTTTACACCGCATCCGGCataaaaaca > 1:1837029‑M2/15‑39 (MQ=255)
ctgccacgtatGTTTACACCGCATCCGGCATAAAAACACGCGCACTTtgc < 1:2442155‑M2/39‑2 (MQ=255)
gATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCACTTTGTCAACAATCTGAAACGCCGGAGAttt > 1:4011657/1‑71 (MQ=255)
aGGCGTTTACGCCGCATCCGTCATAAAAA‑ACGCGCACTTTGTCAACAATCTGa < 1:5426096/53‑1 (MQ=255)
ggCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCACTTTGTCAACAATCTGAAACGCCGGAGATTTTtctc < 1:1972496/71‑1 (MQ=255)
ttACGCCGCATCCGGCATAAAAA‑ACGCGCACTTTGTCAACAATCTGaa < 1:4598763/48‑1 (MQ=255)
tACGCCGCATCCGGCATAAACA‑ACGCGCACTTTGTCAGCAAt > 1:1310397/1‑42 (MQ=11)
tACGCCGCATCCGGCATAAACA‑ACGCGCACTTTGTCAGCAATCTGa > 1:1228585/1‑46 (MQ=11)
tACGCCGCATCCGGCATAAACA‑ACGCGCACTTTGTCAGCAATCTGa > 1:1513414/1‑46 (MQ=11)
tACGCCGCATCCGGCATAAACA‑ACGCGCACTTTGTCAGCAATCTGa > 1:1292796/1‑46 (MQ=11)
tACGCCGCATCCGGCATAAACA‑ACGCGCACTTTGTCAGCAATCTGa > 1:222252/1‑46 (MQ=11)
gccgcATCCGGCATAAAAA‑ACGCGCACTTTGTCAACAATCt < 1:1631437/41‑1 (MQ=255)
|
CAGGCCTACCTTTTCCTGCAACACTTTGAATTTATGAGTTTTTGTAGGCTGGATAAGGCGTTTACGCCGCATCCGGCATAAAAA‑ACGCGCACTTTGTCAACAATCTGAAACGCCGGAGATTTTTCTC > minE/1019136‑1019262
|
| 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
