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 |
|
A3 F44 I0 R1
|
30 |
22.2 |
989614 |
86.8% |
858984 |
142.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913 |
1,196,245 |
T→C |
100% |
L375M (TTA→CTG) |
icd → |
isocitrate dehydrogenase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,196,245 | 0 | T | C | 100.0%
| 12.5
/ ‑6.7
| 11 | L375M (TTA→CTG) | icd | isocitrate dehydrogenase |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (6/4); total (6/5) |
| 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. |
AATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGAT > NC_000913/1196114‑1196316
|
aaTGCGCCCTGGTTGAAGCCACCCACGGTACTGCGTTGATATATGTTGTTCAGGACATTGTTAATTCTGGCTCTATGATTCTCTCCGCTGGGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTaaa < 1:402682/143‑1 (MQ=18)
gcCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAACGTAAATCCTGGATCTATTATTCTCTACGCTGAGATGATACTGCGCAATATGGGTTGGACTGAAGCGGCTGACCTGAATGTTAAAGGTAt > 1:57834/1‑143 (MQ=37)
cTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATTCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGATTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGa > 1:236124/1‑143 (MQ=37)
tGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGAACTGAAGAGGCTGACCTGATTGTTAAAGGTATGGaa > 1:289268/1‑143 (MQ=37)
gCCACCCACGGTGCTTCGGCGAAATATGCCGGTCAGGTGAAAGTAAGTCCTGGCGCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAAt < 2:131313/143‑1 (MQ=21)
acGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGACGGCGCACTCAAcgcc > 2:456215/1‑142 (MQ=25)
tgTACTGCGCCGTAATATGCCGGTCAGGACAATGTAATTCGTGTCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCaatgccaa < 1:234541/142‑7 (MQ=18)
ggTACTGCGCCGAAATATGCCCGTCAGGACAAAGTTATTTCTGGTTCTATTATTTTCTCTTCTGTGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCaatgccaa < 1:424646/143‑7 (MQ=17)
cGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGAAAGGCGCAATCAATGCCAAGACCGTAAct > 2:13733/1‑142 (MQ=18)
gACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCt > 2:98627/1‑143 (MQ=11)
tAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTTGATTGAAGCTGCTGTCTTTTTTGTTATAGGTATGGAAGGCGCAATCAAAGCCAAGACCGTAACTTATGACTTCGAACGTCTgatggaa < 1:6129/143‑2 (MQ=14)
|
AATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGAT > NC_000913/1196114‑1196316
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
