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 R2
|
422 |
46.8 |
3726540 |
94.7% |
3529033 |
61.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,846,634 |
Δ1 bp |
100% |
intergenic (‑49/+79) |
ynjI ← / ← topB |
predicted inner membrane protein/DNA topoisomerase III |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,846,634 | 0 | A | . | 94.7%
| 67.0
/ ‑1.9
| 19 | intergenic (‑49/+79) | ynjI/topB | predicted inner membrane protein/DNA topoisomerase III |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base . (6/12); total (6/13) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.11e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| 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. |
TTGTAATAAAACTTTTTTCATCACATTCCCTGTTATTACATACTTTAGAGGCGATAATTTTATCCATGCAAAAAAAATATCCAACGAATTTTCTTGATCCGCTGGATATTTCAGAATATGACTCG > W3110S.gb/1846565‑1846689
|
ttGTAATAAAACTTTTTTCATCACATTCCCTGTTATTACATACTTTAGAGGCGATAATTTTATCCATGCa > 1:2802874/1‑70 (MQ=255)
taataaAACTTTTTTCATCACATTCCCTGTTATTACATACTTTAGAGGCGATAATTTTATCCATGCaaaaa < 1:2658044/71‑1 (MQ=255)
cTTTTTTCATCACATTCCCTGTTATTACATACTTTAGAGGCGATAATTTTATCCATGC‑AAAAAAATATCCa < 1:2891231/71‑1 (MQ=255)
cTTTTTTCATCACATTCCCTGTTATTACATACTTTAGAGGCGATAATTTTATCCATGC‑AAAAAAATATCCa < 1:753187/71‑1 (MQ=255)
tttttCATCACATTCCCTGTTATTACATACTTTAGAGGCGATAATTTTATCCATGCaaaaaaat > 1:1565780/1‑63 (MQ=255)
ttCATCACAATCCCTGTTATTACATACTTTAGAGGCGATAATTTTATCCATGCaaaaa < 1:225688/58‑1 (MQ=255)
acaTTCCCTGTTATTACATACTTTAGAGGCGATAATTTTATCCATGC‑AAAAAAATATCCAACGAATTTTCt < 1:1564193/71‑1 (MQ=255)
acaTTCCCTGTTATTACATACTTTAGAGGCGATAATTTTATCCATGC‑AAAAAAATATCCAACGAATTTTCt > 1:2390633/1‑71 (MQ=255)
aTTCCCTGTTATTACATACTTTAGAGGCGATAATTTTATCCATGC‑AAAAAAATATCCAACGAATTTTCTTg < 1:3720601/71‑1 (MQ=255)
aTTCCCTGTTATTACATACTTTAGAGGCGATAATTTTATCCATGC‑AAAAAAATATCCAACGAATTTTCTTg < 1:1227671/71‑1 (MQ=255)
gTTATTACATACTTTAGAGGCGATAATTTTATCCATGC‑AAAAAAATATCCAACGAATTTTCTTGATCCGCt > 1:1972788/1‑71 (MQ=255)
gTTATTACATACTTTAGAGGCGATAATTTTATCCATGC‑AAAAAAATATCCAACGAATTTTCTTGATCCGCt > 1:1964078/1‑71 (MQ=255)
attaCATACTTTAGAGGCGATAATTTTATCCATGC‑AAAAAAATATCCAACGAATTTTCTTGATCCGCTGGa > 1:1987979/1‑71 (MQ=255)
ttAGAGGCGATAATTTTATCCATGC‑AAAAAAATATCCAACGAATTTTCTTGATCCGCTGGATATTTCAGaa > 1:189329/1‑71 (MQ=255)
ttAGAGGCGATAATTTTATCCATGC‑AAAAAAATATCCAACGAATTTTCTTGATCCGCTGGATATTTCAGaa > 1:3631042/1‑71 (MQ=255)
agagGCGATAATTTTATCCATGCAAAAAAAATATCCAACGAATTTTCTTGATCCGCTGGATATTTCAGaa < 1:1718080/70‑1 (MQ=255)
gCGATAATTTTATCCATGC‑AAAAAAATATCCAACGAATTTTCTTGATCCGCTg < 1:3036447/53‑1 (MQ=255)
cGATAATTTTATCCATGC‑AAAAAAATATCCAACGAATTTTCTTGATCCGCTGGATATTTCAg < 1:1777192/62‑1 (MQ=255)
cGATAATTTTATCCATGC‑AAAAAAATATCCAACGAATTTTCTTGATCCGCTGGATATTTCAg < 1:1409605/62‑1 (MQ=255)
aTAATTTTATCCATGC‑AAAAAAATATCCAACGAAt < 1:3637513/35‑1 (MQ=38)
tAATTTTATCCATGC‑AAAAAAATATCCAACGAATTTTCTTGATCCGCTGGATATTTCAGAATATGACTCg < 1:773662/70‑1 (MQ=255)
aTTTTATCCATGC‑AAAAAAATATCCAACGAATTTTCTTGa < 1:2431685/40‑1 (MQ=39)
aTTTTATCCATGC‑AAAAAAATATCCAACGAATTTTCTTGa < 1:2354491/40‑1 (MQ=39)
|
TTGTAATAAAACTTTTTTCATCACATTCCCTGTTATTACATACTTTAGAGGCGATAATTTTATCCATGCAAAAAAAATATCCAACGAATTTTCTTGATCCGCTGGATATTTCAGAATATGACTCG > W3110S.gb/1846565‑1846689
|
| 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
