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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
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 | 87.5%
| 52.7
/ 3.1
| 24 | E117G (GAA→GGA) | ygbA | nitrous oxide‑stimulated promoter family protein |
| Reads supporting (aligned to +/- strand): ref base T (1/2); new base C (9/12); total (10/14) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.98e-01 |
CACGGATGAAGCGGCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATTCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTAAGATCGGATG > NZ_CP009273/2849732‑2849904
|
cACGGATGAAGCGGCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGa > 1:195728/1‑90 (MQ=255)
ggCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGACTGTCCGGCATACTATCCATGAGGTTTTTTCGGa > 2:742934/1‑90 (MQ=255)
gCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGAc < 1:333962/90‑1 (MQ=255)
gCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGAc > 1:6985/1‑90 (MQ=255)
gCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGAc < 1:267142/90‑1 (MQ=255)
cTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACg > 1:503409/1‑90 (MQ=255)
aaTCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGc < 2:29033/90‑1 (MQ=255)
aTCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATTCATGAGGTTTTTTCGGACGATATTTTTCCGGCa > 2:746390/1‑90 (MQ=255)
aTCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCa < 1:594559/90‑1 (MQ=255)
aaCTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGa > 1:368458/1‑90 (MQ=255)
cAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATTCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCtt < 1:307988/90‑1 (MQ=255)
aTTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTc < 2:178458/90‑1 (MQ=255)
aGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCgatgaga < 2:265172/90‑1 (MQ=255)
aTCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCgatgagatg < 1:578765/90‑1 (MQ=255)
ccTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCa < 2:393806/90‑1 (MQ=255)
cTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCAc < 2:786392/90‑1 (MQ=255)
cTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCAc < 2:585064/90‑1 (MQ=255)
gTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACgg > 2:705749/1‑90 (MQ=255)
tCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGt > 2:27608/1‑90 (MQ=255)
tCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGt > 2:380972/1‑90 (MQ=255)
ccGGCATACTATTCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGtt < 1:746390/90‑1 (MQ=255)
tACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTAAGATc < 1:705749/90‑1 (MQ=255)
cTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCa < 1:201693/38‑1 (MQ=38)
cTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCa > 2:201693/1‑38 (MQ=38)
ttCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTAAGATCGGATg < 2:141135/90‑1 (MQ=255)
|
CACGGATGAAGCGGCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATTCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTAAGATCGGATG > NZ_CP009273/2849732‑2849904
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ 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
GACCCTGCTGTCACGGATGAAGCGGCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATTCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTAAGATCGGATGACGCC > NZ_CP009273/2849721‑2849909
|
GACCCTGCTGTCACGGATGAAGCGGCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATG < SRR3722079.42833/100‑1 (MQ=60)
ACCCTGCTGTCACGGATGAAGCGGCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGA > SRR3722079.197418/1‑100 (MQ=60)
GGATGAAGCGGCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGAC > SRR3722079.7046/1‑100 (MQ=60)
GATGAAGCGGCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACG > SRR3722079.507949/1‑100 (MQ=60)
GCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTC < SRR3722079.269380/100‑1 (MQ=60)
GCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTC < SRR3722079.336613/100‑1 (MQ=60)
cctctctggtctcgtgggctcggagatgtgtataagagacagGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCAC < SRR3722079.203434/58‑1 (MQ=60)
ATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCAC < SRR3722079.600514/100‑1 (MQ=60)
GCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGA > SRR3722079.371386/1‑100 (MQ=60)
CAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATTCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATG < SRR3722079.310493/100‑1 (MQ=60)
ATCTGCCTGTCCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTT < SRR3722079.584494/100‑1 (MQ=60)
CCGGCATACTATTCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTAAGATCGGAT < SRR3722079.754364/100‑1 (MQ=60)
CCGGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTAAGATCGGAT > SRR3722079.771729/1‑100 (MQ=60)
GGCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTAAGATCGGATGA > SRR3722079.5812/1‑100 (MQ=60)
GCATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTAAGATCGGATGAC > SRR3722079.655584/1‑100 (MQ=60)
ATACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTAAGATCGGATGACGC > SRR3722079.699352/1‑100 (MQ=60)
TACTATCCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTAAGATCGGATGACGCC < SRR3722079.713235/100‑1 (MQ=60)
|
GACCCTGCTGTCACGGATGAAGCGGCTGGGAATTGATAAATCGGCATTGATTTAACTGCAAATTGCCGGACAGATCTGCCTGTCCGGCATACTATTCATGAGGTTTTTTCGGACGATATTTTTCCGGCAGTTCTGGCACCGGACGCTTGTCATCGATGAGATGACGCACGGTTAAGATCGGATGACGCC > NZ_CP009273/2849721‑2849909
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
