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 R1
|
82 |
77.9 |
2158605 |
86.8% |
1873669 |
62.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,712,069:1 |
+T |
100% |
intergenic (‑16/+81) |
yphF ← / ← yphG |
predicted sugar transporter subunit/conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,712,069 | 1 | . | T | 96.0%
| 84.1
/ ‑2.6
| 25 | intergenic (‑16/+81) | yphF/yphG | predicted sugar transporter subunit/conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base T (24/0); total (25/0) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
CATTTTTGTAGGCATAGAGCCTCCTGTAGGG‑TTTTT‑ATTAACAACGGCTTATTCTAATTATTTTGT > minE/1712039‑1712104
|
cATTTTTGTAGGCATAGAGCCTCCTGTAGGGTTTTTT‑ATTAACAACGGCTTATTCTAATTATTTtgt > 1:1183730/1‑67 (MQ=255)
cATTTTTGTAGGCATAGAGCCTCCTGTAGGGTTTTTT‑ATTAACAACGGCTTATTCTAATTATTTtgt > 1:933705/1‑67 (MQ=255)
cATTTTTGTAGGCATAGAGCCTCCTGTAGGGTTTTTT‑ATTAACAACGGCTTATTCTAATTATTTtgt > 1:920190/1‑67 (MQ=255)
cATTTTTGTAGGCATAGAGCCTCCTGTAGGGTTTTTT‑ATTAACAACGGCTTATTCTAATTATTTtgt > 1:82099/1‑67 (MQ=255)
cATTTTTGTAGGCATAGAGCCTCCTGTAGGGTTTTTT‑ATTAACAACGGCTTATTCTAATTATTTtgt > 1:775630/1‑67 (MQ=255)
cATTTTTGTAGGCATAGAGCCTCCTGTAGGGTTTTTT‑ATTAACAACGGCTTATTCTAATTATTTtgt > 1:741943/1‑67 (MQ=255)
cATTTTTGTAGGCATAGAGCCTCCTGTAGGGTTTTTT‑ATTAACAACGGCTTATTCTAATTATTTtgt > 1:551901/1‑67 (MQ=255)
cATTTTTGTAGGCATAGAGCCTCCTGTAGGGTTTTTT‑ATTAACAACGGCTTATTCTAATTATTTtgt > 1:411854/1‑67 (MQ=255)
cATTTTTGTAGGCATAGAGCCTCCTGTAGGGTTTTTT‑ATTAACAACGGCTTATTCTAATTATTTtgt > 1:356627/1‑67 (MQ=255)
cATTTTTGTAGGCATAGAGCCTCCTGTAGGGTTTTTT‑ATTAACAACGGCTTATTCTAATTATTTtgt > 1:226845/1‑67 (MQ=255)
cATTTTTGTAGGCATAGAGCCTCCTGTAGGGTTTTTT‑ATTAACAACGGCTTATTCTAATTATTTtgt > 1:2011874/1‑67 (MQ=255)
cATTTTTGTAGGCATAGAGCCTCCTGTAGGGTTTTTT‑ATTAACAACGGCTTATTCTAATTATTTtgt > 1:184286/1‑67 (MQ=255)
cATTTTTGTAGGCATAGAGCCTCCTGTAGGGTTTTTT‑ATTAACAACGGCTTATTCTAATTATTTtgt > 1:1700706/1‑67 (MQ=255)
cATTTTTGTAGGCATAGAGCCTCCTGTAGGGTTTTTT‑ATTAACAACGGCTTATTCTAATTATTTtgt > 1:1666306/1‑67 (MQ=255)
cATTTTTGTAGGCATAGAGCCTCCTGTAGGGTTTTTT‑ATTAACAACGGCTTATTCTAATTATTTtgt > 1:160744/1‑67 (MQ=255)
cATTTTTGTAGGCATAGAGCCTCCTGTAGGGTTTTTT‑ATTAACAACGGCTTATTCTAATTATTTtgt > 1:1576220/1‑67 (MQ=255)
cATTTTTGTAGGCATAGAGCCTCCTGTAGGGTTTTTT‑ATTAACAACGGCTTATTCTAATTATTTtgt > 1:1547894/1‑67 (MQ=255)
cATTTTTGTAGGCATAGAGCCTCCTGTAGGGTTTTTT‑ATTAACAACGGCTTATTCTAATTATTTtgt > 1:1535382/1‑67 (MQ=255)
cATTTTTGTAGGCATAGAGCCTCCTGTAGGGTTTTTT‑ATTAACAACGGCTTATTCTAATTATTTtgt > 1:1466956/1‑67 (MQ=255)
cATTTTTGTAGGCATAGAGCCTCCTGTAGGGTTTTTT‑ATTAACAACGGCTTATTCTAATTATTTtgt > 1:138845/1‑67 (MQ=255)
cATTTTTGTAGGCATAGAGCCTCCTGTAGGGTTTTTT‑ATTAACAACGGCTTATTCTAATTATTTtgt > 1:1192189/1‑67 (MQ=255)
cATTTTTGTAGGCATAGAGCCTCCTGTAGGGTTTTTT‑ATTAACAACGGCTTATTCTAATTATTTtgt > 1:1106343/1‑67 (MQ=255)
cATTTTTGTAGGCATAGAGCCTCCTGTAGGGTTTTTT‑ATTAACAACGGCTTATTCTAATTATTTtg > 1:1687009/1‑66 (MQ=255)
cATTTTTGTAGGCATAGAGCCTCCTGTAGGG‑TTTTTCATTAACAACGGCTTATTCTAATTATTTtgt > 1:953654/1‑67 (MQ=255)
cATTTTTGTAGGCAAAGAGCCTCCTGTAGGGTTTTTT‑ATTAACAACGGCTTATTCTAATTATTTtgt > 1:1697043/1‑67 (MQ=255)
|
CATTTTTGTAGGCATAGAGCCTCCTGTAGGG‑TTTTT‑ATTAACAACGGCTTATTCTAATTATTTTGT > minE/1712039‑1712104
|
| 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
