Table 2.

Mean missingness in tumor and adjacent normal tissue across different RNA species.

RNA type	The total number of RNAs of the given type	Mean number of samples with missing valuesa
		Tumor	Adjacent normal
protein coding	19,509	9.01 ± 0.13	8.2 ± 0.12
lncRNA	17,141	31.24 ± 0.18	29.52 ± 0.18
processed pseudogene	9148	41.2 ± 0.24	39.68 ± 0.23
unprocessed pseudogene	1879	49.05 ± 0.44	47.11 ± 0.45
misc RNA	1173	50.12 ± 0.54	49.08 ± 0.53
TEC—to be experimentally confirmed	1011	23.83 ± 0.75	21.61 ± 0.72
Transcribed unprocessed pseudogene	904	25.05 ± 0.83	23.66 ± 0.81
Transcribed processed pseudogene	489	25.89 ± 1.08	24.51 ± 1.06
Transcribed unitary pseudogene	148	24.15 ± 1.97	24.52 ± 1.99
IG V pseudogene	134	61.55 ± 0.65	62.73 ± 0.39
IG V gene	134	28.16 ± 1.92	30.14 ± 2.03
TR V gene	105	36.03 ± 1.71	39.44 ± 1.70
Unitary pseudogene	85	43.32 ± 2.19	40.28 ± 2.27
snRNA	56	63.51 ± 0.55	63.21 ± 0.52
snoRNA	52	51.48 ± 2.96	52.28 ± 3.06
TR V pseudogene	27	60.33 ± 1.31	59.77 ± 1.62
Artifact	25	29 ± 4.71	30.64 ± 4.86
IG C pseudogene	9	46.55 ± 7.72	53.11 ± 6.99
Pseudogene	6	38.83 ± 10.63	41.66 ± 10.78
IG C gene	6	5.66 ± 2.84	7.33 ± 4.78
TR C gene	6	2.66 ± 1.85	1 ± 0.51
scaRNA-Small Cajal body-specific RNA	3	54.66 ± 10.34	56.66 ± 8.83
miRNA	3	59.33 ± 1.33	63.33 ± 1.33
Translated unprocessed pseudogene	3	19.33 ± 7.96	18.66 ± 9.17
Ribozyme	2	64	64
Translated processed pseudogene	2	32.5 ± 15.5	29.5 ± 8.5
IG pseudogene	1	65	66
IG J gene	1	66	65
scRNA—A small conditional RNA	1	1	0
All groups	52,063	25.58 ± 0.11	24.28 ± 0.11

^aMean missingness was estimated as the number of samples with missing values in a given RNA type, averaged over all RNAs of a given type.