High frequencies of AGY, but not TCN Ser codons among germline-encoded CDR sequences of IgV-region genes. (A) Ratio observed/expected for AGY and TCN Ser codons in human and mouse IgV-region genes. Germline CDRs and FRs were defined using the Kabat numbering system. Expected ratio was defined by frequencies of 52,926 mouse codons and 40,662,582 human codons at http://www.kazusa.or.jp/codon/. (B). Total numbers of AGY or TCN Ser codons per germline-encoded CDR sequences. Box plots were generated as indicated in Section “Materials and Methods.” Briefly, the center line indicates the median; box limits indicate the 25th and 75th percentiles; whiskers extend to minimum and maximum values, and crosses represent sample means. Notches represent the 95% confidence interval for each median. (C) Donut graphs represent the number of CDR1&2 AGY Ser codons minus the number of TCN Ser codons for a given gene. The gray, white, and black areas denote the number of IgV genes in which AGY Ser codon numbers are greater than, equal to, or less than TCN codon numbers respectively. Number of sequences indicated in center. p values were determined using a two-tailed paired t-test. ***p < 0.0001.