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 F2 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,425,778 |
T→C |
E215G (GAA→GGA) |
folC ← |
bifunctional tetrahydrofolate synthase/dihydrofolate synthase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,425,778 | 0 | T | C | 100.0%
| 38.7
/ NA
| 13 | E215G (GAA→GGA) | folC | bifunctional tetrahydrofolate synthase/dihydrofolate synthase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (11/2); total (11/2) |
GCATCGCTAAACGCCCAGTCATGATCGGTGACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTTCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTGCT > NZ_CP009273/2425700‑2425858
|
gCATCGCTAAACGCCCAGTCATGATCGGTGACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCcaca < 2:550373/90‑1 (MQ=255)
gCTAAACGCCCAGTCATGATCGGTGACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGc > 1:705419/1‑90 (MQ=255)
cccAGTCATGATCGGTGACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAg > 1:389964/1‑90 (MQ=255)
tGATCGGTGACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCAtt > 1:410548/1‑90 (MQ=255)
gTGACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGc > 1:557871/1‑90 (MQ=255)
aCTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCg > 2:486295/1‑90 (MQ=255)
aCGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGtttt > 2:433975/1‑90 (MQ=255)
ccGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCt > 2:512992/1‑90 (MQ=255)
gTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTg > 1:309603/1‑90 (MQ=255)
gTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTg > 1:354750/1‑90 (MQ=255)
gTGCACCTTTTCACTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTg > 1:692063/1‑90 (MQ=255)
tGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTGc < 1:433975/90‑1 (MQ=255)
gCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTGCt > 2:621388/1‑90 (MQ=255)
|
GCATCGCTAAACGCCCAGTCATGATCGGTGACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTTCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTGCT > NZ_CP009273/2425700‑2425858
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATTTTCCAGCGTGCCGTGAGCATCGCTAAACGCCCAGTCATGATCGGTGACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTTCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTGCTTTCTCGCGACCAA > NZ_CP009273/2425681‑2425871
|
ATTTTCCAGCGTGCCGTGAGCATCGCTAAACGCCCAGTCATGATCGGTGACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCC < SRR3722112.716413/100‑1 (MQ=60)
CGTGAGCATCGCTAAACGCCCAGTCATGATCGGTGACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGC > SRR3722112.716438/1‑100 (MQ=60)
TCGCTAAACGCCCAGTCATGATCGGTGACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAG > SRR3722112.395061/1‑100 (MQ=60)
CGCCCAGTCATGATCGGTGACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATT > SRR3722112.415980/1‑100 (MQ=60)
GTCATGATCGGTGACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGC > SRR3722112.566325/1‑100 (MQ=60)
GATCGGTGACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCctgtctcttatacacatctgacgctgccgacgaat > SRR3722112.343723/1‑65 (MQ=60)
CGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTG > SRR3722112.313151/1‑100 (MQ=60)
CGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTG > SRR3722112.359256/1‑100 (MQ=60)
CGTTGTAACAGTGCACCTTTTCACTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTG > SRR3722112.702872/1‑100 (MQ=60)
TGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTGCTTTCTCGCGA < SRR3722112.439904/100‑1 (MQ=60)
GCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTGCTTTCTCGCGAC > SRR3722112.72698/1‑100 (MQ=60)
CACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTGCTTTCTCGCGACC > SRR3722112.18421/1‑100 (MQ=60)
CCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTGCTTTCTCGCGACCAA > SRR3722112.459773/1‑100 (MQ=60)
|
ATTTTCCAGCGTGCCGTGAGCATCGCTAAACGCCCAGTCATGATCGGTGACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTTCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTGCTTTCTCGCGACCAA > NZ_CP009273/2425681‑2425871
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
