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 I231 R1
|
218 |
12.8 |
703680 |
97.2% |
683976 |
86.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,849,816 |
T→C |
E117G (GAA→GGA) |
ygbA ← |
nitrous oxide‑stimulated promoter family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,849,816 | 0 | T | C | 100.0%
| 40.7
/ NA
| 13 | E117G (GAA→GGA) | ygbA | nitrous oxide‑stimulated promoter family protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (6/7); total (6/7) |
CACGGATGAAGCGGCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATTCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTA > NZ_CP009273/2849732‑2849894
|
cACGGATGAAGCGGCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGa > 1:308104/1‑90 (MQ=255)
cACGGATGAAGCGGCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGa > 2:46265/1‑90 (MQ=255)
gCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGAc < 1:309757/90‑1 (MQ=255)
gATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTc > 2:120033/1‑90 (MQ=255)
aaaTCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGata < 1:85979/81‑1 (MQ=255)
aaaTCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGata > 2:85979/1‑81 (MQ=255)
gCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTc < 1:256119/90‑1 (MQ=255)
cAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCtt > 2:313248/1‑90 (MQ=255)
gCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGTACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATc < 2:307039/90‑1 (MQ=255)
ggACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCgat < 1:18313/90‑1 (MQ=255)
gATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCgatgagat > 1:224245/1‑90 (MQ=255)
ccTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCa < 2:262190/90‑1 (MQ=255)
cGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTa < 1:313248/90‑1 (MQ=255)
|
CACGGATGAAGCGGCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATTCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTA > NZ_CP009273/2849732‑2849894
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ 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
ACCCTGCTGTCACGGATGAAGCGGCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATTCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTAAGATCGGATG > NZ_CP009273/2849722‑2849904
|
ACCCTGCTGTCACGGATGAAGCGGCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGA > SRR3722116.312654/1‑100 (MQ=60)
GCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTC < SRR3722116.314331/100‑1 (MQ=60)
GGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGC < SRR3722116.87047/100‑1 (MQ=60)
GCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGA < SRR3722116.259762/100‑1 (MQ=60)
TTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGAT > SRR3722116.227231/1‑100 (MQ=60)
GGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGC < SRR3722116.18559/100‑1 (MQ=60)
GTCCGGCATACTATCTATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTAAGATCGG > SRR3722116.246501/1‑100 (MQ=60)
CGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTAAGATCGGATG < SRR3722116.317881/100‑1 (MQ=60)
|
ACCCTGCTGTCACGGATGAAGCGGCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATTCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTAAGATCGGATG > NZ_CP009273/2849722‑2849904
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
