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 |
2,888,711 |
A→G |
V143A (GTC→GCC) |
ygcQ ← |
electron transfer flavoprotein subunit alpha/FixB family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,888,711 | 0 | A | G | 79.2%
| 37.4
/ 8.6
| 24 | V143A (GTC→GCC) | ygcQ | electron transfer flavoprotein subunit alpha/FixB family protein |
| Reads supporting (aligned to +/- strand): ref base A (4/1); new base G (12/7); total (16/8) |
| Fisher's exact test for biased strand distribution p-value = 6.31e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.16e-01 |
GCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGACAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGAAAGGCATAGC > NZ_CP009273/2888625‑2888791
|
gCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCaa < 1:9194/90‑1 (MQ=255)
tGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGACAATGTTCAgtt > 1:134906/1‑90 (MQ=255)
gCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGCGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAgttgt < 2:442976/90‑1 (MQ=255)
cTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGttgttg < 1:227982/90‑1 (MQ=255)
cAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCa > 1:401574/1‑90 (MQ=255)
cAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCa > 1:64624/1‑90 (MQ=255)
cAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCa > 1:836719/1‑90 (MQ=255)
aaTGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGACAATGTTCAGTTGTTGCATTCCa > 1:606636/1‑90 (MQ=255)
aTGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCag < 1:481821/90‑1 (MQ=255)
gTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCaa > 2:382102/1‑65 (MQ=255)
gTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCaa < 1:382102/65‑1 (MQ=255)
gTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAggg > 1:62423/1‑90 (MQ=255)
aaCCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGAcg > 1:716185/1‑90 (MQ=255)
agccagTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGcc < 1:94875/90‑1 (MQ=255)
gccagTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCa > 1:14212/1‑90 (MQ=255)
gccagTCCGGAAGCGCACCCGGGACAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCa > 1:227342/1‑90 (MQ=255)
ccagTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAg < 2:117447/90‑1 (MQ=255)
gTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGa > 2:70233/1‑90 (MQ=255)
tCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGaa > 1:21397/1‑90 (MQ=255)
tCCGGAAGCGCACCCGGGACAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGaa < 2:325038/90‑1 (MQ=255)
gAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGAAAGGc > 2:584588/1‑90 (MQ=255)
gcACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGAAAGGCATAGc > 1:729874/1‑90 (MQ=255)
gcACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGAAAGGCATAGc > 1:530222/1‑90 (MQ=255)
gcACCCGGGACAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGAAAGGCATAGc > 1:740619/1‑90 (MQ=255)
|
GCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGACAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGAAAGGCATAGC > NZ_CP009273/2888625‑2888791
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 31 ≤ 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
AGCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGACAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGAAAGGCATAGC > NZ_CP009273/2888624‑2888791
|
AGCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGACAATGTTCAGTT > SRR3722079.136042/1‑100 (MQ=60)
gtgtataagagacagCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTG < SRR3722079.385215/85‑1 (MQ=60)
GCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTG < SRR3722079.9267/100‑1 (MQ=60)
CGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCA > SRR3722079.845675/1‑100 (MQ=60)
CGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCA > SRR3722079.404962/1‑100 (MQ=60)
CGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCA > SRR3722079.65152/1‑100 (MQ=60)
GGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGACAATGTTCAGTTGTTGCATTCCA > SRR3722079.612755/1‑100 (MQ=60)
CTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAG < SRR3722079.229915/100‑1 (MQ=60)
CAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGG > SRR3722079.62931/1‑100 (MQ=60)
ATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGT < SRR3722079.486034/100‑1 (MQ=60)
CCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACG > SRR3722079.723825/1‑100 (MQ=60)
GTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCA > SRR3722079.14316/1‑100 (MQ=60)
GTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGACAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCA > SRR3722079.229272/1‑100 (MQ=60)
AACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGAA > SRR3722079.21546/1‑100 (MQ=60)
AGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGAAAGGC < SRR3722079.95620/100‑1 (MQ=60)
GTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGAAAGGCATAGC > SRR3722079.535166/1‑100 (MQ=60)
GTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGAAAGGCATAGC > SRR3722079.737678/1‑100 (MQ=60)
GTCCGGAAGCGCACCCGGGACAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGAAAGGCATAGC > SRR3722079.748536/1‑100 (MQ=60)
|
AGCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGACAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGAAAGGCATAGC > NZ_CP009273/2888624‑2888791
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
