Table 4 Lifted-over gene annotation statistics

# protein-coding genes Bcop_v1

23,117

16,546

# genes lifted over to Bcop_v2

23,115 (99.99%)

16,542 (99.98%)

# genes not lifted over to Bcop_v2

2 (0.01%)

4 (0.02%)

# transcripts Bcop_v1

28,870

28,473

# transcripts lifted over to Bcop_v2

28,866 (99.99%)

28,464 (99.97%)

# transcripts not lifted over to Bcop_v2

4 (0.01%)

9 (0.03%)

# lifted over transcript sequences identical after liftover

28,813 (99.82%)

28,388 (99.73%)

# lifted over transcripts that yield identical protein sequence after liftover

28,817 (99.83%)

28,396 (99.76%)

# lifted over transcript sequences changed after liftover

53 (0.18%)

76 (0.27%)

# lifted over transcripts that yield changed protein sequence after liftover

49 (0.17%)

68 (0.24%)

# lifted over genes where all transcript isoform sequences are identical before and after liftover

23,083 (99.86%)

16,512 (99.82%)

# lifted over genes where all transcript isoforms yield same protein sequences after liftover

23,084 (99.87%)

16,516 (99.84%)

# lifted over genes where a subset of transcript isoforms sequences is identical before and after liftover

10 (0.04%)

3 (0.02%)

# lifted over genes where a subset of transcript isoforms yield same protein sequences after liftover

10 (0.04%)

4 (0.02%)

# lifted over genes where all transcript isoform sequences differ before and after liftover

22 (0.1%)

27 (0.16%)

# lifted over genes where all transcript isoforms yield changed protein sequences after liftover

21 (0.09%)

22 (0.13%)