Percentage of mutations (≥5%) emerged in the genome of A/PR/8/34 strain (CBER stock) obtained by sequencing five times its RNA library by HiSeq and MiSeq.

<p>Notes: MiSeq values that differ from HiSeq's values are presented in parentheses. These mutation percentages were calculated per comparison to their published sequences. (See accession numbers in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138650#sec002" target="_blank">Materials and Methods</a> paragraph.) nt: Nucleotide, aa: Amino-acid.</p

Percentage of mutations (≥5%) emerged in A/PR/8/34 viruses 1 and 3 genomes that were subjected to RNA library preparation followed by HiSeq sequencing.

<p>Note: These mutation percentages were calculated per comparison of A/PR/8/34 strains 1 and 3 genomes with the corresponding published sequences. (See accession numbers in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138650#sec002" target="_blank">Materials and Methods</a> paragraph.) nt: Nucleotide, aa: Amino-acid.</p

Mutation percentages (≥5%) emerged in HA and NA of X-179A viruses passaged in eggs.

<p>Notes: The percentages obtained from RNA library followed by HiSeq sequencing are presented without parentheses or brackets. The percentages obtained from RNA library followed by MiSeq sequencing are presented in parentheses. The percentages obtained from DNA library followed by HiSeq sequencing are presented in brackets. These mutation percentages were calculated per comparison with the corresponding expanded progenitor. (See accession numbers in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138650#sec002" target="_blank">Materials and Methods</a>.) aa: Amino-acid, nt: Nucleotide.</p

Mutation percentages (≥5%) emerged in HA and NA of X-181 viruses passaged in eggs.

<p>Notes: The percentages obtained from RNA library followed by HiSeq sequencing are presented without parentheses or brackets. The percentages obtained from RNA library followed by MiSeq sequencing are presented in parentheses. The percentages obtained from DNA library followed by HiSeq sequencing are presented in brackets. These mutation percentages were calculated per comparison with the corresponding expanded progenitor. (See accession numbers in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138650#sec002" target="_blank">Materials and Methods</a>.) aa: Amino-acid, nt: Nucleotide.</p

Viruses of A/California/07/2009 vaccines, and A/PR/8/34 and wild type A/California/07/2009 viruses used for deep sequencing analysis.

<p>*: A/PR/8/34 virus stock was passaged 13 times in eggs, and the last passaged virus was passaged one time (passage 14) separately in 2 different eggs, the 2 harvested viruses are designated as A/PR/8/34-1 and A/PR/8/34-3.</p><p>Note: CBER: Center for Biologics Evaluation and Research at US Food and Drug Administration.</p

HiSeq sequencing of RNA Library prepared from A/Ca/07/2009 (H1N1) virus.

<p>*: Count of nucleotide location started 20 nucleotides (UTR) before the starting codon AUG.</p><p>Note: These mutation percentages were calculated per comparison of A/California/07/2009 (H1N1) genome with its published sequence. (See accession numbers in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0138650#sec002" target="_blank">Materials and Methods</a> paragraph.) aa: Amino acid, nt: Nucleotide.</p

A: Simultaneous RT-PCR amplification of the eight segments of A/California/07/2009 (H1N1) vaccine viruses using Phusion DNA polymerase, 1: 1 kb DNA Ladder, 2: X-181-M1, 3: X-179A-M1, 4: X-181-M2, 5: X-179A-M2, 6: X-181-M3, 7: X-179A-M4, 8: 1 kb DNA Ladder, 9: 1 kb DNA Ladder, 10: 121XP-M4, 11: X-181-M4, 12: X-179A-M3, 13: X-179A-M5, 14: X-179A, 15: X-181, 16: Negative control (H₂O). B: Simultaneous RT-PCR amplification of the eight segments of A/California/07/2009 (H1N1) vaccine viruses using Thermo Scientist Extensor Mix, 1: 1 kb DNA Ladder, 2: X-181-M1, 3: X-179A-M1, 4: X-181-M2, 5: X-179A-M2, 6: X-181-M3, 7: X-179A-M4, 8: Negative control (H₂O), 9: 1 kb DNA Ladder, 10: 121XP-M4, 11: X-181-M4, 12: X-179A-M3, 13: X-179A-M5, 14: X-179A, 15: X-181, 16: Negative control (H₂O). C: The distribution amount of sequencing reads between the eight segments of influenza virus using different approaches of library preparation followed by Illumina HiSeq sequencing.

<p>A: Simultaneous RT-PCR amplification of the eight segments of A/California/07/2009 (H1N1) vaccine viruses using Phusion DNA polymerase, 1: 1 kb DNA Ladder, 2: X-181-M1, 3: X-179A-M1, 4: X-181-M2, 5: X-179A-M2, 6: X-181-M3, 7: X-179A-M4, 8: 1 kb DNA Ladder, 9: 1 kb DNA Ladder, 10: 121XP-M4, 11: X-181-M4, 12: X-179A-M3, 13: X-179A-M5, 14: X-179A, 15: X-181, 16: Negative control (H₂O). B: Simultaneous RT-PCR amplification of the eight segments of A/California/07/2009 (H1N1) vaccine viruses using Thermo Scientist Extensor Mix, 1: 1 kb DNA Ladder, 2: X-181-M1, 3: X-179A-M1, 4: X-181-M2, 5: X-179A-M2, 6: X-181-M3, 7: X-179A-M4, 8: Negative control (H₂O), 9: 1 kb DNA Ladder, 10: 121XP-M4, 11: X-181-M4, 12: X-179A-M3, 13: X-179A-M5, 14: X-179A, 15: X-181, 16: Negative control (H₂O). C: The distribution amount of sequencing reads between the eight segments of influenza virus using different approaches of library preparation followed by Illumina HiSeq sequencing.</p

Effects of the eEF1 complex mutants on mis-reading of near- and non-cognate codons.

<p>Misreading of the non-cognate UCU and near-cognate AGC codons by mutant forms of eEF1A (Panel A), or by isogenic strains with <i>tef3Δ, tef4Δ</i>, or <i>tef3Δ tef4Δ</i> double null mutants or <i>tef5Δ</i> strains expressing the K120R S121Δ I122Δ allele compared to isogenic wild-type strain (Panel B). Panel C. Misreading of all seven missense codons by cells lacking both forms of eEF1Bγ (<i>tef3Δ tef4Δ</i>). Effects of the indicated mutants are depicted as fold of isogenic wild-type cells. ** indicates <i>p</i> values of <0.01; * indicates <i>p</i> values of <0.05.</p

Characterization of alleles of <i>RPL5.</i>

<p>Panel A. Effects of the K27E rpl5 mutanton misreading of seven missense codons. Effects on the indicated missense reporters are depicted as fold of isogenic wild-type cells. ** indicates p values of <0.01. Panel B. Paromomycin dilution spot assays. Ten-fold dilutions (10⁶→10¹ CFU) of logarithmically growing cells were arrayed onto H-leu medium containing paromomycin (1 mg/ml) or no drug control plates. Cells were grown at 25°C for 3 days.</p

Effects of selected alleles of genes on mis-reading of non-cognate and near-cognate mutations at codon 218 of firefly luciferase.

<p>Effects of selected alleles of genes on mis-reading of non-cognate and near-cognate mutations at codon 218 of firefly luciferase.</p