Analysis of the Codon Usage Pattern of HA and NA Genes of H7N9 Influenza A Virus
Abstract
:1. Introduction
2. Results
2.1. Phylogenetic Analyses of the HA and NA Genes of H7N9
2.2. Trends of Codon Usage Patterns Based on Different Classifications of HA and NA
2.3. Nucleotide Composition
2.4. Lower Codon Usage Bias in HA and NA Gene
2.5. RSCU Value of HA and NA Genes
2.6. Factors Driving Codon Usage Bias
2.7. The HA and NA Genes of H7N9 Virus Are Highly Adapted to Gallus gallus
2.8. Strong Selection Pressure of Homo Sapiens on H7N9
3. Discussion
4. Material and Methods
4.1. Data Sequences
4.2. Phylogenetic Analysis
4.3. Correspondence Analysis
4.4. Codon Usage Bias Index
4.4.1. Nucleotide Composition
4.4.2. Relative Synonymous Codon Usage Analysis
4.4.3. Effective Number of Codons Analysis
4.5. Factors Mediating Codon Usage Bias
4.5.1. ENC-Plot Analysis
4.5.2. Parity Rule 2 Analysis (PR2)
4.5.3. Neutrality Analysis
4.6. Potential Relationship between Host and Virus
4.6.1. Codon Adaptation Index
4.6.2. Relative Codon Deoptimization Index
4.6.3. Similarity Index
4.6.4. CpG Dinucleotides Frequency
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Gene | Composition of A | Composition of A3 | GC1s | GC2s | GC3s |
---|---|---|---|---|---|
HA | 34.68% ± 0.21 | 48.14% ± 0.99 | 50.05% ± 0.268 | 41.20% ± 0.277 | 34.43% ± 0.796 |
NA | 35.2% ± 0.20 | 49.42% ± 0.613 | 43.51% ± 0.398 | 47.26% ± 0.333 | 39.03% ± 0.624 |
(A)HA | All | Host | Pathogenicity | Wave | Reference Host | ||||||||
Codon | Avian | Human | Environment | High | Low | Wave 1 | Wave 2 | Wave 3 | Wave 4 | Wave 5 | Gallus gallus | Homo sapiens | |
UUU(F) | 0.69 | 0.71 | 0.68 | 0.67 | 0.64 | 0.69 | 0.72 | 0.72 | 0.68 | 0.65 | 0.64 | 0.91 | 0.93 |
UUC(F) | 1.31 | 1.29 | 1.32 | 1.33 | 1.36 | 1.31 | 1.28 | 1.28 | 1.32 | 1.35 | 1.36 | 1.09 | 1.07 |
UUA(L) | 0.5 | 0.52 | 0.48 | 0.49 | 0.49 | 0.5 | 0.46 | 0.51 | 0.5 | 0.48 | 0.48 | 0.45 | 0.46 |
UUG(L) | 0.48 | 0.48 | 0.48 | 0.49 | 0.57 | 0.47 | 0.46 | 0.48 | 0.48 | 0.48 | 0.49 | 0.81 | 0.77 |
CUU(L) | 0.67 | 0.65 | 0.67 | 0.71 | 0.81 | 0.66 | 0.62 | 0.64 | 0.68 | 0.64 | 0.72 | 0.80 | 0.79 |
CUC(L) | 0.91 | 0.87 | 0.92 | 0.93 | 0.98 | 0.9 | 0.92 | 0.85 | 0.93 | 0.94 | 0.95 | 1.08 | 1.17 |
CUA(L) | 1.55 | 1.59 | 1.54 | 1.46 | 1.3 | 1.56 | 1.69 | 1.68 | 1.45 | 1.43 | 1.41 | 0.38 | 0.43 |
CUG(L) | 1.9 | 1.89 | 1.9 | 1.92 | 1.85 | 1.9 | 1.85 | 1.84 | 1.95 | 2.03 | 1.95 | 2.48 | 2.37 |
AUU(I) | 1.09 | 1.11 | 1.08 | 1.08 | 1.06 | 1.09 | 1.12 | 1.11 | 1.09 | 1.06 | 1.05 | 1.06 | 1.08 |
AUC(I) | 0.61 | 0.61 | 0.61 | 0.59 | 0.56 | 0.61 | 0.62 | 0.63 | 0.6 | 0.58 | 0.59 | 1.39 | 1.41 |
AUA(I) | 1.31 | 1.28 | 1.31 | 1.33 | 1.38 | 1.3 | 1.26 | 1.27 | 1.31 | 1.36 | 1.36 | 0.55 | 0.51 |
GUU(V) | 0.93 | 0.91 | 0.94 | 0.97 | 1.04 | 0.93 | 0.88 | 0.89 | 0.94 | 0.98 | 1 | 0.84 | 0.73 |
GUC(V) | 0.75 | 0.75 | 0.75 | 0.74 | 0.7 | 0.75 | 0.75 | 0.75 | 0.75 | 0.76 | 0.75 | 0.87 | 0.95 |
GUA(V) | 1.17 | 1.22 | 1.15 | 1.11 | 0.98 | 1.18 | 1.25 | 1.23 | 1.2 | 1.09 | 1.03 | 0.50 | 0.47 |
GUG(V) | 1.15 | 1.12 | 1.16 | 1.18 | 1.28 | 1.14 | 1.12 | 1.13 | 1.11 | 1.17 | 1.21 | 1.80 | 1.85 |
UCU(S) | 0.88 | 0.91 | 0.87 | 0.87 | 0.94 | 0.88 | 0.9 | 0.9 | 0.91 | 0.83 | 0.82 | 1.09 | 1.13 |
UCC(S) | 0.19 | 0.16 | 0.2 | 0.23 | 0.19 | 0.19 | 0.14 | 0.15 | 0.16 | 0.27 | 0.27 | 1.21 | 1.31 |
UCA(S) | 1.78 | 1.79 | 1.77 | 1.76 | 1.74 | 1.78 | 1.8 | 1.8 | 1.76 | 1.74 | 1.74 | 0.89 | 0.90 |
UCG(S) | 0.22 | 0.19 | 0.24 | 0.26 | 0.3 | 0.22 | 0.15 | 0.16 | 0.27 | 0.31 | 0.32 | 0.40 | 0.33 |
AGU(S) | 1.74 | 1.76 | 1.74 | 1.69 | 1.72 | 1.74 | 1.81 | 1.75 | 1.73 | 1.75 | 1.68 | 0.86 | 0.90 |
AGC(S) | 1.19 | 1.2 | 1.19 | 1.2 | 1.11 | 1.2 | 1.2 | 1.24 | 1.16 | 1.09 | 1.17 | 1.55 | 1.44 |
CCU(P) | 0.77 | 0.71 | 0.8 | 0.8 | 0.67 | 0.77 | 0.71 | 0.71 | 0.74 | 0.87 | 0.9 | 1.10 | 1.15 |
CCC(P) | 0.43 | 0.49 | 0.4 | 0.41 | 0.62 | 0.42 | 0.47 | 0.47 | 0.47 | 0.31 | 0.31 | 1.22 | 1.29 |
CCA(P) | 2.11 | 2.1 | 2.11 | 2.1 | 2.04 | 2.11 | 2.11 | 2.11 | 2.08 | 2.12 | 2.11 | 1.13 | 1.11 |
CCG(P) | 0.7 | 0.71 | 0.69 | 0.69 | 0.66 | 0.7 | 0.71 | 0.71 | 0.7 | 0.7 | 0.67 | 0.56 | 0.45 |
ACU(T) | 1.36 | 1.38 | 1.35 | 1.34 | 1.32 | 1.36 | 1.41 | 1.38 | 1.39 | 1.38 | 1.3 | 0.99 | 0.99 |
ACC(T) | 0.73 | 0.72 | 0.73 | 0.76 | 0.79 | 0.72 | 0.7 | 0.71 | 0.72 | 0.69 | 0.76 | 1.23 | 1.42 |
ACA(T) | 1.88 | 1.88 | 1.89 | 1.88 | 1.78 | 1.89 | 1.88 | 1.88 | 1.88 | 1.92 | 1.91 | 1.20 | 1.14 |
ACG(T) | 0.03 | 0.02 | 0.04 | 0.03 | 0.12 | 0.03 | 0 | 0.03 | 0.01 | 0.01 | 0.03 | 0.57 | 0.46 |
GCU(A) | 1.24 | 1.24 | 1.24 | 1.22 | 1.24 | 1.24 | 1.23 | 1.24 | 1.24 | 1.25 | 1.25 | 1.16 | 1.06 |
GCC(A) | 0.56 | 0.56 | 0.56 | 0.57 | 0.55 | 0.56 | 0.55 | 0.55 | 0.55 | 0.56 | 0.57 | 1.27 | 1.60 |
GCA(A) | 1.88 | 1.89 | 1.87 | 1.87 | 1.89 | 1.88 | 1.89 | 1.9 | 1.88 | 1.85 | 1.85 | 1.06 | 0.91 |
GCG(A) | 0.33 | 0.32 | 0.33 | 0.34 | 0.33 | 0.33 | 0.33 | 0.32 | 0.33 | 0.34 | 0.33 | 0.51 | 0.42 |
UAU(Y) | 1.23 | 1.2 | 1.25 | 1.25 | 1.2 | 1.24 | 1.2 | 1.21 | 1.2 | 1.29 | 1.31 | 0.80 | 0.89 |
UAC(Y) | 0.77 | 0.8 | 0.75 | 0.75 | 0.8 | 0.76 | 0.8 | 0.79 | 0.8 | 0.71 | 0.69 | 1.20 | 1.11 |
CAU(H) | 1.37 | 1.39 | 1.37 | 1.36 | 1.4 | 1.37 | 1.4 | 1.4 | 1.4 | 1.4 | 1.33 | 0.80 | 0.84 |
CAC(H) | 0.63 | 0.61 | 0.63 | 0.64 | 0.6 | 0.63 | 0.6 | 0.6 | 0.6 | 0.6 | 0.67 | 1.20 | 1.16 |
CAA(Q) | 1.3 | 1.31 | 1.29 | 1.29 | 1.31 | 1.3 | 1.28 | 1.31 | 1.29 | 1.29 | 1.29 | 0.54 | 0.53 |
CAG(Q) | 0.7 | 0.69 | 0.71 | 0.71 | 0.69 | 0.7 | 0.72 | 0.69 | 0.71 | 0.71 | 0.71 | 1.46 | 1.47 |
AAU(N) | 1.28 | 1.28 | 1.28 | 1.29 | 1.32 | 1.28 | 1.29 | 1.27 | 1.29 | 1.27 | 1.27 | 0.86 | 0.94 |
AAC(N) | 0.72 | 0.72 | 0.72 | 0.71 | 0.68 | 0.72 | 0.71 | 0.73 | 0.71 | 0.73 | 0.73 | 1.14 | 1.06 |
AAA(K) | 1.32 | 1.3 | 1.33 | 1.31 | 1.32 | 1.32 | 1.36 | 1.31 | 1.35 | 1.28 | 1.3 | 0.89 | 0.87 |
AAG(K) | 0.68 | 0.7 | 0.67 | 0.69 | 0.68 | 0.68 | 0.64 | 0.69 | 0.65 | 0.72 | 0.7 | 1.11 | 1.13 |
GAU(D) | 1.25 | 1.23 | 1.25 | 1.25 | 1.22 | 1.25 | 1.22 | 1.25 | 1.23 | 1.27 | 1.29 | 1.01 | 0.93 |
GAC(D) | 0.75 | 0.77 | 0.75 | 0.75 | 0.78 | 0.75 | 0.78 | 0.75 | 0.77 | 0.73 | 0.71 | 0.99 | 1.07 |
GAA(E) | 1.38 | 1.4 | 1.37 | 1.37 | 1.44 | 1.38 | 1.4 | 1.4 | 1.39 | 1.35 | 1.34 | 0.86 | 0.84 |
GAG(E) | 0.62 | 0.6 | 0.63 | 0.63 | 0.56 | 0.62 | 0.6 | 0.6 | 0.61 | 0.65 | 0.66 | 1.14 | 1.16 |
UGU(C) | 1.37 | 1.37 | 1.37 | 1.37 | 1.38 | 1.37 | 1.37 | 1.37 | 1.38 | 1.36 | 1.36 | 0.80 | 0.91 |
UGC(C) | 0.63 | 0.63 | 0.63 | 0.63 | 0.62 | 0.63 | 0.63 | 0.63 | 0.62 | 0.64 | 0.64 | 1.20 | 1.09 |
CGU(R) | 0.2 | 0.2 | 0.2 | 0.2 | 0.18 | 0.2 | 0.2 | 0.21 | 0.2 | 0.2 | 0.2 | 0.59 | 0.48 |
CGC(R) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1.14 | 1.10 |
CGA(R) | 0.56 | 0.6 | 0.55 | 0.52 | 0.55 | 0.56 | 0.6 | 0.62 | 0.59 | 0.58 | 0.47 | 0.58 | 0.65 |
CGG(R) | 0.51 | 0.44 | 0.54 | 0.57 | 0.56 | 0.51 | 0.4 | 0.41 | 0.39 | 0.58 | 0.71 | 1.07 | 1.21 |
AGA(R) | 3.31 | 3.28 | 3.32 | 3.33 | 3.4 | 3.3 | 3.23 | 3.33 | 3.25 | 3.35 | 3.4 | 1.34 | 1.29 |
AGG(R) | 1.42 | 1.47 | 1.4 | 1.38 | 1.31 | 1.42 | 1.57 | 1.43 | 1.57 | 1.3 | 1.22 | 1.29 | 1.27 |
GGU(G) | 0.67 | 0.65 | 0.67 | 0.68 | 0.65 | 0.67 | 0.64 | 0.64 | 0.66 | 0.71 | 0.71 | 0.70 | 0.65 |
GGC(G) | 0.48 | 0.48 | 0.47 | 0.48 | 0.49 | 0.48 | 0.48 | 0.48 | 0.48 | 0.48 | 0.47 | 1.22 | 1.35 |
GGA(G) | 1.89 | 1.97 | 1.87 | 1.83 | 1.88 | 1.9 | 2 | 2 | 1.87 | 1.71 | 1.73 | 1.09 | 1.00 |
GGG(G) | 0.96 | 0.91 | 0.98 | 1.01 | 0.98 | 0.96 | 0.88 | 0.88 | 0.99 | 1.09 | 1.09 | 0.99 | 1.00 |
(B)NA | All | Host | Pathogenicity | Wave | Reference host | ||||||||
Codon | Avian | Human | Environment | High | Low | Wave 1 | Wave 2 | Wave 3 | Wave 4 | Wave 5 | Gallus gallus | Homo sapiens | |
UUU(F) | 0.49 | 0.5 | 0.47 | 0.51 | 0.46 | 0.51 | 0.44 | 0.48 | 0.46 | 0.46 | 0.55 | 0.91 | 0.93 |
UUC(F) | 1.51 | 1.5 | 1.53 | 1.49 | 1.54 | 1.49 | 1.56 | 1.52 | 1.54 | 1.54 | 1.45 | 1.09 | 1.07 |
UUA(L) | 1.02 | 1.03 | 1.01 | 1.06 | 1.03 | 1.03 | 0.98 | 1 | 1 | 1.14 | 1.06 | 0.45 | 0.46 |
UUG(L) | 0.95 | 0.95 | 0.98 | 0.91 | 0.79 | 0.94 | 1 | 1.01 | 1 | 1.02 | 0.86 | 0.81 | 0.77 |
CUU(L) | 0.26 | 0.26 | 0.24 | 0.25 | 0.26 | 0.27 | 0.25 | 0.25 | 0.25 | 0.25 | 0.28 | 0.80 | 0.79 |
CUC(L) | 0.99 | 0.99 | 1.01 | 0.99 | 1.03 | 0.98 | 1 | 1 | 1 | 1 | 0.97 | 1.08 | 1.17 |
CUA(L) | 1.51 | 1.51 | 1.51 | 1.51 | 1.4 | 1.52 | 1.52 | 1.5 | 1.49 | 1.35 | 1.54 | 0.38 | 0.43 |
CUG(L) | 1.26 | 1.26 | 1.25 | 1.29 | 1.49 | 1.26 | 1.25 | 1.25 | 1.26 | 1.23 | 1.28 | 2.48 | 2.37 |
AUU(I) | 0.82 | 0.83 | 0.8 | 0.84 | 0.74 | 0.84 | 0.81 | 0.79 | 0.83 | 0.79 | 0.86 | 1.06 | 1.08 |
AUC(I) | 0.42 | 0.42 | 0.41 | 0.42 | 0.48 | 0.42 | 0.41 | 0.42 | 0.42 | 0.42 | 0.43 | 1.39 | 1.41 |
AUA(I) | 1.76 | 1.75 | 1.79 | 1.74 | 1.78 | 1.74 | 1.78 | 1.79 | 1.76 | 1.79 | 1.7 | 0.55 | 0.51 |
GUU(V) | 0.7 | 0.71 | 0.71 | 0.69 | 0.58 | 0.71 | 0.72 | 0.71 | 0.71 | 0.78 | 0.7 | 0.84 | 0.73 |
GUC(V) | 0.33 | 0.32 | 0.34 | 0.34 | 0.48 | 0.3 | 0.34 | 0.31 | 0.33 | 0.33 | 0.3 | 0.87 | 0.95 |
GUA(V) | 1.66 | 1.68 | 1.64 | 1.65 | 1.66 | 1.66 | 1.73 | 1.64 | 1.71 | 1.67 | 1.64 | 0.50 | 0.47 |
GUG(V) | 1.3 | 1.3 | 1.32 | 1.31 | 1.28 | 1.32 | 1.21 | 1.33 | 1.26 | 1.21 | 1.36 | 1.80 | 1.85 |
UCU(S) | 0.73 | 0.71 | 0.79 | 0.69 | 0.69 | 0.68 | 0.83 | 0.84 | 0.7 | 0.59 | 0.59 | 1.09 | 1.13 |
UCC(S) | 0.46 | 0.48 | 0.44 | 0.48 | 0.43 | 0.49 | 0.42 | 0.42 | 0.45 | 0.53 | 0.54 | 1.21 | 1.31 |
UCA(S) | 2.07 | 2.07 | 2.09 | 2.06 | 2.03 | 2.06 | 2.07 | 2.1 | 2.1 | 2.06 | 2.03 | 0.89 | 0.90 |
UCG(S) | 0.43 | 0.43 | 0.42 | 0.43 | 0.52 | 0.43 | 0.43 | 0.4 | 0.41 | 0.44 | 0.45 | 0.40 | 0.33 |
AGU(S) | 1.19 | 1.21 | 1.13 | 1.23 | 1.23 | 1.24 | 1.11 | 1.09 | 1.24 | 1.37 | 1.32 | 0.86 | 0.90 |
AGC(S) | 1.12 | 1.1 | 1.14 | 1.11 | 1.1 | 1.1 | 1.14 | 1.16 | 1.1 | 1.01 | 1.07 | 1.55 | 1.44 |
CCU(P) | 1.03 | 1.03 | 1.02 | 1.04 | 1.13 | 1.03 | 1 | 0.99 | 1.1 | 1.08 | 1.04 | 1.10 | 1.15 |
CCC(P) | 0.84 | 0.85 | 0.83 | 0.85 | 0.84 | 0.86 | 0.83 | 0.84 | 0.81 | 0.81 | 0.88 | 1.22 | 1.29 |
CCA(P) | 1.61 | 1.6 | 1.65 | 1.59 | 1.66 | 1.58 | 1.67 | 1.68 | 1.61 | 1.62 | 1.51 | 1.13 | 1.11 |
CCG(P) | 0.52 | 0.53 | 0.5 | 0.51 | 0.37 | 0.54 | 0.5 | 0.49 | 0.49 | 0.49 | 0.57 | 0.56 | 0.45 |
ACU(T) | 1.05 | 1.02 | 1.12 | 1.02 | 1.01 | 1.02 | 1.07 | 1.12 | 1.06 | 1.05 | 0.96 | 0.99 | 0.99 |
ACC(T) | 0.54 | 0.55 | 0.51 | 0.54 | 0.51 | 0.55 | 0.55 | 0.51 | 0.53 | 0.54 | 0.57 | 1.23 | 1.42 |
ACA(T) | 2.4 | 2.42 | 2.36 | 2.43 | 2.47 | 2.42 | 2.38 | 2.37 | 2.4 | 2.4 | 2.45 | 1.20 | 1.14 |
ACG(T) | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0 | 0 | 0.01 | 0.01 | 0.02 | 0.57 | 0.46 |
GCU(A) | 1.2 | 1.2 | 1.21 | 1.18 | 1.17 | 1.19 | 1.21 | 1.22 | 1.18 | 1.18 | 1.18 | 1.16 | 1.06 |
GCC(A) | 0.87 | 0.87 | 0.87 | 0.89 | 0.93 | 0.86 | 0.87 | 0.86 | 0.89 | 0.88 | 0.86 | 1.27 | 1.60 |
GCA(A) | 1.76 | 1.76 | 1.75 | 1.76 | 1.71 | 1.77 | 1.74 | 1.74 | 1.75 | 1.76 | 1.8 | 1.06 | 0.91 |
GCG(A) | 0.17 | 0.17 | 0.17 | 0.17 | 0.2 | 0.17 | 0.18 | 0.17 | 0.18 | 0.17 | 0.16 | 0.51 | 0.42 |
UAU(Y) | 1.21 | 1.21 | 1.2 | 1.22 | 1.2 | 1.22 | 1.2 | 1.2 | 1.21 | 1.23 | 1.22 | 0.80 | 0.89 |
UAC(Y) | 0.79 | 0.79 | 0.8 | 0.78 | 0.8 | 0.78 | 0.8 | 0.8 | 0.79 | 0.77 | 0.78 | 1.20 | 1.11 |
CAU(H) | 0.65 | 0.64 | 0.67 | 0.66 | 0.73 | 0.63 | 0.67 | 0.67 | 0.7 | 0.62 | 0.6 | 0.80 | 0.84 |
CAC(H) | 1.35 | 1.36 | 1.33 | 1.34 | 1.27 | 1.37 | 1.33 | 1.33 | 1.3 | 1.38 | 1.4 | 1.20 | 1.16 |
CAA(Q) | 1.08 | 1.08 | 1.08 | 1.08 | 1.08 | 1.08 | 1.05 | 1.08 | 1.09 | 1.07 | 1.08 | 0.54 | 0.53 |
CAG(Q) | 0.92 | 0.92 | 0.92 | 0.92 | 0.92 | 0.92 | 0.95 | 0.92 | 0.91 | 0.93 | 0.92 | 1.46 | 1.47 |
AAU(N) | 0.96 | 0.96 | 0.97 | 0.94 | 0.86 | 0.95 | 0.99 | 0.98 | 0.96 | 0.94 | 0.92 | 0.86 | 0.94 |
AAC(N) | 1.04 | 1.04 | 1.03 | 1.06 | 1.14 | 1.05 | 1.01 | 1.02 | 1.04 | 1.06 | 1.08 | 1.14 | 1.06 |
AAA(K) | 1.26 | 1.26 | 1.26 | 1.26 | 1.31 | 1.25 | 1.29 | 1.26 | 1.28 | 1.28 | 1.23 | 0.89 | 0.87 |
AAG(K) | 0.74 | 0.74 | 0.74 | 0.74 | 0.69 | 0.75 | 0.71 | 0.74 | 0.72 | 0.72 | 0.77 | 1.11 | 1.13 |
GAU(D) | 0.97 | 0.98 | 0.96 | 0.98 | 0.93 | 0.98 | 0.97 | 0.95 | 0.92 | 0.95 | 1.01 | 1.01 | 0.93 |
GAC(D) | 1.03 | 1.02 | 1.04 | 1.02 | 1.07 | 1.02 | 1.03 | 1.05 | 1.08 | 1.05 | 0.99 | 0.99 | 1.07 |
GAA(E) | 1.33 | 1.35 | 1.3 | 1.35 | 1.35 | 1.35 | 1.27 | 1.26 | 1.4 | 1.43 | 1.37 | 0.86 | 0.84 |
GAG(E) | 0.67 | 0.65 | 0.7 | 0.65 | 0.65 | 0.65 | 0.73 | 0.74 | 0.6 | 0.57 | 0.63 | 1.14 | 1.16 |
UGU(C) | 0.65 | 0.65 | 0.67 | 0.64 | 0.67 | 0.64 | 0.66 | 0.66 | 0.67 | 0.67 | 0.62 | 0.80 | 0.91 |
UGC(C) | 1.35 | 1.35 | 1.33 | 1.36 | 1.33 | 1.36 | 1.34 | 1.34 | 1.33 | 1.33 | 1.38 | 1.20 | 1.09 |
CGU(R) | 0.24 | 0.24 | 0.24 | 0.24 | 0.26 | 0.24 | 0.24 | 0.24 | 0.24 | 0.24 | 0.25 | 0.59 | 0.48 |
CGC(R) | 0.25 | 0.24 | 0.25 | 0.27 | 0.45 | 0.24 | 0.24 | 0.24 | 0.32 | 0.24 | 0.23 | 1.14 | 1.10 |
CGA(R) | 0.96 | 0.96 | 0.95 | 0.96 | 0.98 | 0.96 | 0.97 | 0.96 | 0.94 | 0.98 | 0.97 | 0.58 | 0.65 |
CGG(R) | 0.01 | 0.01 | 0.01 | 0.02 | 0.01 | 0.01 | 0 | 0 | 0 | 0 | 0.02 | 1.07 | 1.21 |
AGA(R) | 2.43 | 2.41 | 2.49 | 2.42 | 2.46 | 2.4 | 2.4 | 2.49 | 2.38 | 2.4 | 2.38 | 1.34 | 1.29 |
AGG(R) | 2.11 | 2.13 | 2.06 | 2.09 | 1.85 | 2.14 | 2.16 | 2.06 | 2.12 | 2.13 | 2.15 | 1.29 | 1.27 |
GGU(G) | 0.46 | 0.46 | 0.45 | 0.45 | 0.44 | 0.46 | 0.45 | 0.47 | 0.46 | 0.47 | 0.46 | 0.70 | 0.65 |
GGC(G) | 0.55 | 0.55 | 0.54 | 0.54 | 0.54 | 0.54 | 0.54 | 0.54 | 0.55 | 0.54 | 0.55 | 1.22 | 1.35 |
GGA(G) | 1.7 | 1.67 | 1.76 | 1.63 | 1.47 | 1.65 | 1.78 | 1.82 | 1.61 | 1.56 | 1.56 | 1.09 | 1.00 |
GGG(G) | 1.3 | 1.32 | 1.24 | 1.38 | 1.55 | 1.34 | 1.23 | 1.17 | 1.38 | 1.43 | 1.43 | 0.99 | 1.00 |
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Sun, J.; Zhao, W.; Wang, R.; Zhang, W.; Li, G.; Lu, M.; Shao, Y.; Yang, Y.; Wang, N.; Gao, Q.; et al. Analysis of the Codon Usage Pattern of HA and NA Genes of H7N9 Influenza A Virus. Int. J. Mol. Sci. 2020, 21, 7129. https://doi.org/10.3390/ijms21197129
Sun J, Zhao W, Wang R, Zhang W, Li G, Lu M, Shao Y, Yang Y, Wang N, Gao Q, et al. Analysis of the Codon Usage Pattern of HA and NA Genes of H7N9 Influenza A Virus. International Journal of Molecular Sciences. 2020; 21(19):7129. https://doi.org/10.3390/ijms21197129
Chicago/Turabian StyleSun, Jiumeng, Wen Zhao, Ruyi Wang, Wenyan Zhang, Gairu Li, Meng Lu, Yuekun Shao, Yichen Yang, Ningning Wang, Qi Gao, and et al. 2020. "Analysis of the Codon Usage Pattern of HA and NA Genes of H7N9 Influenza A Virus" International Journal of Molecular Sciences 21, no. 19: 7129. https://doi.org/10.3390/ijms21197129