Summary
If you make 13,142,501 円 a year living in Japan, you will be taxed 3,787,972 円. That means that your net pay will be 9,354,530 円 per year, or 779,544 円 per month. Your average tax rate is 28.8% 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 37.16 円, hence, your net pay will only increase by 62.84 円.
Bonus Example
A 1,000 円 bonus will generate an extra 628 円 of net incomes. A 5,000 円 bonus will generate an extra 3,142 円 of net incomes.