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 F1 I2 R1
|
524 |
31.4 |
1748232 |
97.8% |
1709770 |
80.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,066,740 |
A→G |
G194G (GGT→GGC) |
insH‑6 ← |
CP4‑44 prophage; IS5 transposase and trans‑activator |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,066,740 | 0 | A | G | 94.7%
| 50.8
/ ‑3.7
| 19 | G194G (GGT→GGC) | insH‑6 | CP4‑44 prophage; IS5 transposase and trans‑activator |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base G (9/9); total (9/10) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01 |
TACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACACCAATGTGGGCCTTCATGCCAAAGTGCCACTGATTGCCTTTCTTGGTCTGATGCATCTCCGGATC > NC_000913/2066664‑2066805
|
tACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACGCCaa > 1:351387/1‑81 (MQ=255)
aCCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACGCCAAt > 2:351393/1‑81 (MQ=255)
aCCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACGCCAAt > 1:351382/1‑81 (MQ=255)
aTTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACGCCAATGTGGGcc < 1:351353/79‑1 (MQ=255)
aTTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACGCCAATGTGGGCCtt < 2:351354/81‑1 (MQ=255)
gAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACGCCAATGTGGGCCTTCa < 1:351355/80‑1 (MQ=255)
aTGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACGCCAATGTGGGCCTTCATGCCaa < 2:351356/80‑1 (MQ=255)
aTGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACGCCAATGTGGGCCTTCATGCCa > 1:351402/1‑79 (MQ=255)
cTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACGCCAATGTGGGCCTTCATGCCAAAGTg > 2:351381/1‑81 (MQ=255)
gCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACGCCAATGTGGGCCTTCATGCCAAAGTGCCACTg < 2:351357/80‑1 (MQ=255)
ccGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACGCCAATGTGGGCCTTCATGCCAAAGTGCCACTGAt < 1:351358/81‑1 (MQ=255)
ggtggtGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACGCCAATGTGGGCCTTCATGCCAAAGTGCCACTGATTGcc > 1:351406/1‑81 (MQ=255)
tgACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACACCAATGTGGGCCTTCATGCCAAAGTGCCACTGATTGCCTTTCt < 1:351359/81‑1 (MQ=38)
aCTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACGCCAATGTGGGCCTTCATGCCAAAGTGCCACTGATTGCCTTTCTTg > 1:351398/1‑81 (MQ=255)
ggCTGTGGGTCAGGCCGCTCTTGGCATCGACGCCAATGTGGGCCTTCATGCCAAAGTGCCACTGATTGCCTTTCTTGGTCt < 2:351360/81‑1 (MQ=18)
gCTGTGGGTCAGGCCGCTCTTGGCATCGACGCCAATGTGGGCCTTCATGCCAAAGTGCCACTGATTGCCTTTCTTGGTCt > 1:351404/1‑80 (MQ=21)
tCAGGCCGCTCTTGGCATCGACGCCAATGTGGGCCTTCATGCCAAAGTGCCACTGATTGCCTTTCTTGGTCTGATGCAtct < 2:351361/81‑1 (MQ=18)
gCTCTTGGCATCGACGCCAATGTGGGCCTTCATGCCAAAGTGCCACTGATTGCCTTTCTTGGTCTGATGCATCTCCGGATc < 1:351362/81‑1 (MQ=14)
gCTCTTGGCATCGACGCCAATGTGGGCCTTCATGCCAAAGTGCCACTGATTGCCTTTCTTGGTCTGATGCATCTCCGGATc > 2:351397/1‑81 (MQ=14)
|
TACCCAGCTGATTGAGGTCATGCTCGTTGGCCGCGGTGGTGACTAGGCTGTGGGTCAGGCCGCTCTTGGCATCGACACCAATGTGGGCCTTCATGCCAAAGTGCCACTGATTGCCTTTCTTGGTCTGATGCATCTCCGGATC > NC_000913/2066664‑2066805
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
