Summary
If you make 12,876,900 円 a year living in Japan, you will be taxed 3,689,290 円. That means that your net pay will be 9,187,610 円 per year, or 765,634 円 per month. Your average tax rate is 28.7% and your marginal tax rate is 37.2%. This marginal tax rate means that your immediate additional income will be taxed at this rate. For instance, an increase of 100 円 in your salary will be taxed 37.15 円, hence, your net pay will only increase by 62.85 円.
Bonus Example
A 1,000 円 bonus will generate an extra 629 円 of net incomes. A 5,000 円 bonus will generate an extra 3,143 円 of net incomes.