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 I225 R1
|
227 |
21.4 |
1179702 |
97.1% |
1145490 |
86.5 |
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 | 100.0%
| 40.4
/ NA
| 14 | V143A (GTC→GCC) | ygcQ | electron transfer flavoprotein subunit alpha/FixB family protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (7/7); total (7/7) |
AGCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGACAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGAAAGGCATAGCGGG > NZ_CP009273/2888624‑2888794
|
aGCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCa < 2:13802/90‑1 (MQ=255)
gTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCa > 1:411771/1‑90 (MQ=255)
cAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCa > 1:488121/1‑90 (MQ=255)
aaTGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCa > 1:158853/1‑90 (MQ=255)
ggTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAgg > 2:388669/1‑90 (MQ=255)
cgcgGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCAt > 1:228223/1‑79 (MQ=255)
cgcgGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCAt < 2:228223/79‑1 (MQ=255)
tccAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTc < 2:92765/88‑1 (MQ=255)
aTCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCgctgc > 2:320674/1‑90 (MQ=255)
tAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGAc < 2:411771/90‑1 (MQ=255)
aaCCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGAcg > 1:469103/1‑90 (MQ=255)
agccagTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGcc < 2:245855/90‑1 (MQ=255)
aaGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGAAAGGCa < 2:7805/90‑1 (MQ=255)
cccGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGAAAGGCATAGCggg < 1:452636/90‑1 (MQ=255)
|
AGCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGACAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGAAAGGCATAGCGGG > NZ_CP009273/2888624‑2888794
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 30 ≤ 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
CCCACCACCAGCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGACAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGAAAGGCATAGCGGGCGTTTTTCTGTTT > NZ_CP009273/2888615‑2888807
|
CCCACCACCAGCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAA < SRR3722109.161029/100‑1 (MQ=60)
CCCACCAGCCCCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGT < SRR3722109.255955/100‑1 (MQ=60)
ACCAGCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCA > SRR3722109.417776/1‑100 (MQ=60)
CAGCACCCGTTTGGCCTCAGATAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGT < SRR3722109.147927/100‑1 (MQ=60)
CGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCA > SRR3722109.495483/1‑100 (MQ=60)
GGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCA > SRR3722109.160818/1‑100 (MQ=60)
GCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCC > SRR3722109.230933/1‑100 (MQ=60)
CCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACG > SRR3722109.476165/1‑100 (MQ=60)
CCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGAAAGGCATAGCGGGCGTTTTTCTG > SRR3722109.277146/1‑100 (MQ=60)
CCCGGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGAAAGGCATAGCGGGCGTTTTTCTG < SRR3722109.459415/100‑1 (MQ=60)
GGGGCAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGAAAGGCATAGCGGGCGTTTTTCTGTTT < SRR3722109.106238/100‑1 (MQ=60)
|
CCCACCACCAGCACCCGTCTGGCCTCAGCTAATGGGTCGCGGGTAACATTTTTCAGATCCTCTGTGCTAACCAGCCAGTCCGGAAGCGCACCCGGGACAATGTTCAGTTGTTGCATTCCAGAGGGCAACGTGGCGTTTTTCGCTGCTCCCGCCTGACGCGCCAGGGAAAGGCATAGCGGGCGTTTTTCTGTTT > NZ_CP009273/2888615‑2888807
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
