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 |
1,683,445:1 |
+CCA |
100% |
coding (1529/4962 nt) |
yfhM ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,683,445 | 1 | . | C | 88.9%
| 25.8
/ ‑2.2
| 9 | coding (1529/4962 nt) | yfhM | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base C (8/0); total (9/0) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| 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. |
| * | minE | 1,683,445 | 2 | . | C | 88.9%
| 20.5
/ ‑2.2
| 9 | coding (1529/4962 nt) | yfhM | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base C (8/0); total (9/0) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.68e-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. |
| * | minE | 1,683,445 | 3 | . | A | 88.9%
| 22.5
/ ‑1.9
| 9 | coding (1529/4962 nt) | yfhM | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base A (8/0); total (9/0) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CATTAGCAGGTGCACCATACAGGTAGTACC‑‑‑CCACCACGGAGAATTTCACTTCATCTTTCGGCGTTAGCGGGGTTTTCTCA > minE/1683416‑1683495
|||
cATTAGCAGGTGCACCATACAGGTAGTACCCCACCACCACGGAGAATTTCACTTCATCTTTCGGc > 1:1049657/1‑65 (MQ=255)
cATTAGCAGGTGCACCATACAGGTAGTACCCCACCACCACGGAGAATTTCACTTCATCTTTCGGc > 1:1489141/1‑65 (MQ=255)
cATTAGCAGGTGCACCATACAGGTAGTACCCCACCACCACGGAGAATTTCACTTCATCTTTCGGc > 1:2134411/1‑65 (MQ=255)
cATTAGCAGGTGCACCATACAGGTAGTACCCCACCACCACGGAGAATTTCACTTCATCTTTCGGc > 1:2136783/1‑65 (MQ=255)
cATTAGCAGGTGCACCATACAGGTAGTACCCCACCACCACGGAGAATTTCACTTCATCTTTCGGc > 1:433969/1‑65 (MQ=255)
cATTAGCAGGTGCACCATACAGGTAGTACCCCACCACCACGGAGAATTTCACTTCATCTTTCGGc > 1:574448/1‑65 (MQ=255)
cATTAGCAGGTGCACCATACAGGTAGTACCCCACCACCACGGAGAATTTCACTTCATCTTTCGGc > 1:715887/1‑65 (MQ=255)
cATTAGCAGGTGCACCATACAGGTAGTACCCCACCACCACGGAGAATTTCACTTCATCTTTCGGc > 1:78248/1‑65 (MQ=255)
aCCATACAGGTAGTACC‑‑‑CCACCACGGAGAATTTCACTTCATCTTTCGGCGTTAGCGTGGTTTTCTCa > 1:1828938/1‑67 (MQ=255)
|||
CATTAGCAGGTGCACCATACAGGTAGTACC‑‑‑CCACCACGGAGAATTTCACTTCATCTTTCGGCGTTAGCGGGGTTTTCTCA > minE/1683416‑1683495
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
