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 I210 R1
|
226 |
19.6 |
1130256 |
95.4% |
1078264 |
84.4 |
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 | 94.7%
| 52.2
/ ‑3.5
| 19 | E215G (GAA→GGA) | folC | bifunctional tetrahydrofolate synthase/dihydrofolate synthase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (14/4); minor base A (1/0); total (15/4) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.88e-01 |
AAACGCCCAGTCATGATCGGTGACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTTCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTGCTTTCTCG > NZ_CP009273/2425708‑2425864
|
aaaCGCCCAGTCATGATCGGTGACGGAATAGTTCCCCTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAAt < 1:359689/90‑1 (MQ=255)
aaaCGCCCAGTCATGATCGGTGACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAAt < 2:129762/90‑1 (MQ=255)
cccAGTCATGATCGGTGACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAg > 2:73531/1‑90 (MQ=255)
aGTCATGATCGGTGACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAg > 2:272154/1‑90 (MQ=255)
gATCGGTGACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCAttt > 1:380772/1‑90 (MQ=255)
gTGACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGc > 2:3731/1‑90 (MQ=255)
gTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAAt > 1:479009/1‑90 (MQ=255)
tCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTg > 1:136758/1‑90 (MQ=255)
cACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGcc < 1:485713/90‑1 (MQ=255)
aCGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGtttt > 2:351511/1‑90 (MQ=255)
aCGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGtttt > 2:7204/1‑90 (MQ=255)
ccGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCt > 1:404294/1‑90 (MQ=255)
cAGTGCACCTTTTCCCTGCGCCACAGCAGCAATGGTAGAATGCATTTCCGGCTCACCGATAATTGCCGGTTTTCCGCTGCGGAAGATGcc < 2:380772/90‑1 (MQ=255)
aGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCt > 2:19280/1‑90 (MQ=255)
aGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCt > 2:253193/1‑90 (MQ=255)
aGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCt > 1:389747/1‑90 (MQ=255)
aGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCt > 1:112002/1‑90 (MQ=255)
gTGCACCTTTTACCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTg > 1:99577/1‑90 (MQ=255)
gCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTGCt > 1:359189/1‑90 (MQ=255)
tttcCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTGCTTTCTcg < 1:533689/90‑1 (MQ=255)
|
AAACGCCCAGTCATGATCGGTGACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTTCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTGCTTTCTCG > NZ_CP009273/2425708‑2425864
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 29 ≤ 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
AAACGCCCAGTCATGATCGGTGACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTTCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTGCTTTCTCGCGACCAATAC > NZ_CP009273/2425708‑2425874
|
AAACGCCCAGTCATGATCGGTGACGGAATAGTTCCCCTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGC < SRR3722092.366331/100‑1 (MQ=60)
GCCCATTCATGATCGGTGACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTT > SRR3722092.387996/1‑100 (MQ=60)
TGACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAAT > SRR3722092.488523/1‑100 (MQ=60)
ACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTG > SRR3722092.139055/1‑100 (MQ=60)
CACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGC < SRR3722092.495363/100‑1 (MQ=60)
ACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCT > SRR3722092.412071/1‑100 (MQ=60)
ACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCT > SRR3722092.113903/1‑100 (MQ=60)
ACGTTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCT > SRR3722092.397181/1‑100 (MQ=60)
CGTTGTAACAGTGCACCTTTTACCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTG > SRR3722092.101279/1‑100 (MQ=60)
TTGTAACAGTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTGCT > SRR3722092.365810/1‑100 (MQ=60)
GTGCACCTTTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTGCTTTCTCGCG > SRR3722092.376917/1‑100 (MQ=60)
TTTCCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTGCTTTCTCGCGACCAATAC < SRR3722092.544394/100‑1 (MQ=60)
|
AAACGCCCAGTCATGATCGGTGACGGAATAGTTCCACTCAACGCCCCGACGTTGTAACAGTGCACCTTTTTCCTGCGCCACATCAGCAATGGTAGAAGGCATTTCCGGCTCACCGACAATTGCCGGTTTTTCGCTGCGGAAGATGCCTGCTTTCTCGCGACCAATAC > NZ_CP009273/2425708‑2425874
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
