Table 1.
Total number of reads aligned to each of the tRNA sequences in the three sequencing runs: S1, S2 and S3. To compensate for the errors due to modifications, a mismatch of 3 was allowed during the alignment. Yeast-Phe1, yeast-Phe2 and E. coli-Lys denote the spike-in tRNAs.
| tRNA | Anticodon | S1 | S2 | S3 | |||
|---|---|---|---|---|---|---|---|
| Total reads | % | Total reads | % | Total reads | % | ||
| Yeast-Phe1 | GAA | 415536 | 746408 | 86629 | |||
| Yeast-Phe2 | GAA | 20535 | 33741 | 7306 | |||
| E. coli-Lys | UUU | 33692 | 21375 | 16073 | |||
| Ala | UGC | 22444 | 0.256 | 12161 | 0.159 | 473 | 0.336 |
| Arg1 | ACG | 59683 | 0.680 | 25693 | 0.336 | 983 | 0.697 |
| Arg2 | CCG | 165 | 0.002 | 173 | 10023 | 11 | 0.008 |
| Arg3 | CCU | 312 | 0.004 | 175 | 0.002 | 18 | 0.013 |
| Arg4 | UCU | 1828 | 0.021 | 513 | 0.007 | 42 | 0.030 |
| Asn | GUU | 2601864 | 29.660 | 6564554 | 85.872 | 91573 | 64.967 |
| Asp | GUC | 756713 | 8.626 | 201852 | 2.640 | 5485 | 3.891 |
| Cys | GCA | 7514 | 0.086 | 4562 | 0.056 | 185 | 0.131 |
| Gln | UUG | 184109 | 2.099 | 42708 | 0.559 | 7656 | 5.432 |
| Glu | UUC | 21639 | 0.247 | 12489 | 0.163 | 822 | 0.583 |
| Gly1 | GCC | 113327 | 1.292 | 32436 | 0.424 | 3435 | 2.437 |
| Gly2 | UCC | 136225 | 1.553 | 57221 | 0.749 | 8634 | 6.125 |
| His | GUG | 120 | 0.001 | 55 | 0.0007 | 22 | 0.016 |
| Ile | GAU | 10788 | 0.123 | 3922 | 0.051 | 211 | 0.150 |
| Leu1 | AAG | 3606 | 0.041 | 2079 | 0.028 | 113 | 0.080 |
| Leu2 | AAG | 5830 | 0.066 | 2239 | 0.029 | 189 | 0.134 |
| Leu3 | CAA | 3080 | 0.035 | 1517 | 0.020 | 89 | 0.063 |
| Leu4 | CAG | 23301 | 0.266 | 6267 | 0.082 | 626 | 0.444 |
| Leu5 | UAA | 3432527 | 39.130 | 137062 | 1.793 | 1804 | 1.280 |
| Leu6 | UAG | 30 | 0.0003 | 3 | 0.0004 | 10 | 0.007 |
| Lys1 | CUU | 212643 | 2.424 | 49224 | 0.644 | 1742 | 1.236 |
| Lys2 | UUU | 22348 | 0.255 | 5645 | 0.074 | 476 | 0.338 |
| Lys3 | UUU | 33144 | 0.378 | 10635 | 0.139 | 211 | 0.150 |
| Met1 | CAU | 7269 | 0.083 | 3059 | 0.040 | 409 | 0.290 |
| Met2 | CAU | 10045 | 0.115 | 5502 | 0.072 | 126 | 0.089 |
| Met3 | CAU | 69730 | 0.795 | 21575 | 0.282 | 2375 | 1.685 |
| Met4 | CAU | 0 | 0 | 1 | 0.0001 | 0 | 0 |
| Phe | GAA | 9304 | 0.106 | 3855 | 0.050 | 235 | 0.167 |
| Pro | UGG | 277237 | 3.160 | 56638 | 0.741 | 1321 | 0.937 |
| Ser1 | CGA | 834 | 0.010 | 181 | 0.002 | 24 | 0.017 |
| Ser2 | GCU | 222 | 0.003 | 81 | 0.001 | 15 | 0.011 |
| Ser3 | GGA | 781 | 0.009 | 802 | 0.010 | 60 | 0.043 |
| Ser4 | UGA | 82156 | 0.937 | 32438 | 0.424 | 2366 | 1.679 |
| Ser5 | UGA | 1558 | 0.018 | 236 | 0.003 | 188 | 0.133 |
| Thr1 | CGU | 7739 | 0.088 | 7418 | 0.097 | 508 | 0.360 |
| Thr2 | GGU | 116 | 0.001 | 121 | 0.002 | 26 | 0.018 |
| Thr3 | UGU | 214805 | 2.449 | 207407 | 2.714 | 3315 | 2.352 |
| Trp | CCA | 389074 | 4.435 | 109560 | 1.433 | 2776 | 1.969 |
| Tyr | GUA | 38613 | 0.440 | 13782 | 0.180 | 1495 | 1.061 |
| Val | UAC | 9440 | 0.108 | 8757 | 0.115 | 906 | 0.643 |