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 F3 I0 R1
|
328 |
90.1 |
2317887 |
85.2% |
1974839 |
62.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,600,586 |
Δ5 bp |
100% |
coding (856‑860/1425 nt) |
murP → |
fused predicted enzyme IIBC components of PTS |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,600,586 | 0 | A | . | 100.0%
| 29.7
/ NA
| 8 | coding (856/1425 nt) | murP | fused predicted enzyme IIBC components of PTS |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (8/0); total (8/0) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| * | minE | 1,600,587 | 0 | T | . | 100.0%
| 29.7
/ NA
| 8 | coding (857/1425 nt) | murP | fused predicted enzyme IIBC components of PTS |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (8/0); total (8/0) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| * | minE | 1,600,588 | 0 | G | . | 100.0%
| 29.7
/ NA
| 8 | coding (858/1425 nt) | murP | fused predicted enzyme IIBC components of PTS |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base . (8/0); total (8/0) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| * | minE | 1,600,589 | 0 | T | . | 100.0%
| 29.7
/ NA
| 8 | coding (859/1425 nt) | murP | fused predicted enzyme IIBC components of PTS |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (8/0); total (8/0) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| * | minE | 1,600,590 | 0 | C | . | 100.0%
| 29.7
/ NA
| 8 | coding (860/1425 nt) | murP | fused predicted enzyme IIBC components of PTS |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (8/0); total (8/0) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GCCGCTGGGTGGCTGGTTATTCGAAGGTATGTCATGGCTGTTTATGCACCTGAACAGTAATC > minE/1600558‑1600619
|||||
gCCGCTGGGTGGCTGGTTATTCGAAGGT‑‑‑‑‑ATGGCTGTTTATGCACCTGAACAGTaa > 1:32821/1‑55 (MQ=255)
gCCGCTGGGTGGCTGGTTATTCGAAGGT‑‑‑‑‑ATGGCTGTTTATGCACCTGAACAGTAATc > 1:1044091/1‑57 (MQ=255)
gCCGCTGGGTGGCTGGTTATTCGAAGGT‑‑‑‑‑ATGGCTGTTTATGCACCTGAACAGTAATc > 1:1069841/1‑57 (MQ=255)
gCCGCTGGGTGGCTGGTTATTCGAAGGT‑‑‑‑‑ATGGCTGTTTATGCACCTGAACAGTAATc > 1:171714/1‑57 (MQ=255)
gCCGCTGGGTGGCTGGTTATTCGAAGGT‑‑‑‑‑ATGGCTGTTTATGCACCTGAACAGTAATc > 1:2095591/1‑57 (MQ=255)
gCCGCTGGGTGGCTGGTTATTCGAAGGT‑‑‑‑‑ATGGCTGTTTATGCACCTGAACAGTAATc > 1:2194277/1‑57 (MQ=255)
gCCGCTGGGTGGCTGGTTATTCGAAGGT‑‑‑‑‑ATGGCTGTTTATGCACCTGAACAGTAATc > 1:316430/1‑57 (MQ=255)
gCCGCTGGGTGGCTGGTTATTCGAAGGT‑‑‑‑‑ATGGCTGTTTATGCACCTGAACAGTAATc > 1:758857/1‑57 (MQ=255)
|||||
GCCGCTGGGTGGCTGGTTATTCGAAGGTATGTCATGGCTGTTTATGCACCTGAACAGTAATC > minE/1600558‑1600619
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
