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 I207 R1
|
218 |
45.0 |
2482936 |
97.1% |
2410930 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,782,276 |
T→G |
V192G (GTG→GGG) |
ppsR → |
posphoenolpyruvate synthetase regulatory kinase/phosphorylase PpsR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,782,276 | 0 | T | G | 100.0%
| 65.9
/ NA
| 20 | V192G (GTG→GGG) | ppsR | posphoenolpyruvate synthetase regulatory kinase/phosphorylase PpsR |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (16/4); total (16/4) |
CCCCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGTGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAG > NZ_CP009273/1782193‑1782358
|
ccccACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTAcc > 2:758939/1‑90 (MQ=255)
ccaccaGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCcg > 1:55498/1‑90 (MQ=255)
ccaccaGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCcg > 2:359386/1‑90 (MQ=255)
gTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGc > 2:725514/1‑90 (MQ=255)
cTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTc > 1:541499/1‑90 (MQ=255)
gTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCaa > 1:814665/1‑90 (MQ=255)
tCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAAcc < 2:710910/90‑1 (MQ=255)
ggCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCt > 2:401684/1‑90 (MQ=255)
gCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCtt < 1:456426/90‑1 (MQ=255)
aTGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAg > 1:435137/1‑90 (MQ=255)
aTGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAg > 1:701824/1‑90 (MQ=255)
gTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGt > 1:1017602/1‑90 (MQ=255)
tATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGtt < 2:701824/90‑1 (MQ=255)
ccGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCgg > 2:262920/1‑90 (MQ=255)
tttATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGaa < 1:483410/90‑1 (MQ=255)
aTTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGt > 2:1139999/1‑90 (MQ=255)
gCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTg > 2:120913/1‑90 (MQ=255)
gCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTg > 1:143948/1‑90 (MQ=255)
tGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTc > 2:331099/1‑90 (MQ=255)
aaTCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAg > 1:456280/1‑90 (MQ=255)
|
CCCCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGTGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAG > NZ_CP009273/1782193‑1782358
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ 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
TCGCTGTGGTAAAACCCCCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGTGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGGAACGTCGGGAGAACAG > NZ_CP009273/1782178‑1782375
|
TCGCTGTGGTAAAACCCCCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGG < SRR3722089.882933/100‑1 (MQ=60)
CGCTGTGGTAAAACCCCCACCAGTCTGTATCTGGAAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGC < SRR3722089.583583/100‑1 (MQ=60)
GTGGTAAAGCCCCCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACC < SRR3722089.472272/100‑1 (MQ=60)
GGTAAAACCCCCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCG > SRR3722089.56184/1‑100 (MQ=60)
CCCCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTC > SRR3722089.547801/1‑100 (MQ=60)
CCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAA > SRR3722089.826063/1‑100 (MQ=60)
GTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAG > SRR3722089.710974/1‑100 (MQ=60)
GTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAG > SRR3722089.440372/1‑100 (MQ=60)
GCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAAT < SRR3722089.461888/100‑1 (MQ=60)
ATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGT > SRR3722089.1032766/1‑100 (MQ=60)
CCCCTTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTG > SRR3722089.145726/1‑100 (MQ=60)
TTTATTGCCGACGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGG < SRR3722089.489151/100‑1 (MQ=60)
CGATATGGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAG > SRR3722089.461738/1‑100 (MQ=60)
GGATAATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGGAACGT > SRR3722089.302087/1‑100 (MQ=60)
ATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACctgtctcttatacacatctgacgctgccgac > SRR3722089.392942/1‑69 (MQ=60)
ATCTGGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGGAACGTCGGGA > SRR3722089.435186/1‑100 (MQ=60)
GGGGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGGAACGTCGGGAGAAC > SRR3722089.128619/1‑100 (MQ=60)
GGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGGAACGTCGGGAGAACAG > SRR3722089.412772/1‑100 (MQ=60)
|
TCGCTGTGGTAAAACCCCCACCAGTCTGTATCTGGCAATGCAGTTTGGTATCCGCGCGGCAAACTACCCCTTTATTGCCGACGATATGGATAATCTGGTGCTACCCGCGTCGCTCAAACCGCTTCAGCATAAATTGTTCGGCCTGACTATCGACCCGGAACGTCTGGCGGCGATTCGCGAGGAACGTCGGGAGAACAG > NZ_CP009273/1782178‑1782375
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
