Table 1 Distribution of mapped reads in different categories of RNAs in the six samples
Sample_name | LTR_Zer1 | LTR_Zer2 | LTR_L1 | LTR_L2 | LTR_01 | LTR02 |
|---|---|---|---|---|---|---|
3prime_overlapping_ncrna | 159 (0.00%) | 180 (0.00%) | 160 (0.00%) | 171 (0.00%) | 180 (0.00%) | 160 (0.00%) |
IG_C_gene | 0 (0.00%) | 2 (0.00%) | 1 (0.00%) | 0 (0.00%) | 3 (0.00%) | 1 (0.00%) |
IG_C_pseudogene | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) |
IG_D_gene | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) |
IG_J_gene | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) |
IG_J_pseudogene | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) |
IG_V_gene | 4 (0.00%) | 2 (0.00%) | 1 (0.00%) | 3 (0.00%) | 1 (0.00%) | 4 (0.00%) |
IG_V_pseudogene | 0 (0.00%) | 0 (0.00%) | 3 (0.00%) | 1 (0.00%) | 0 (0.00%) | 1 (0.00%) |
Mt_rRNA | 1318 (0.00%) | 1488 (0.00%) | 1734 (0.00%) | 1496 (0.00%) | 1342 (0.00%) | 1779 (0.01%) |
Mt_tRNA | 644 (0.00%) | 637 (0.00%) | 692 (0.00%) | 784 (0.00%) | 603 (0.00%) | 668 (0.00%) |
TEC | 5415 (0.01%) | 5636 (0.01%) | 5036 (0.01%) | 5747 (0.01%) | 5685 (0.02%) | 5276 (0.02%) |
TR_C_gene | 32 (0.00%) | 21 (0.00%) | 23 (0.00%) | 29 (0.00%) | 36 (0.00%) | 26 (0.00%) |
TR_D_gene | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) |
TR_J_gene | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) |
TR_J_pseudogene | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) |
TR_V_gene | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 1 (0.00%) | 0 (0.00%) | 0 (0.00%) |
TR_V_pseudogene | 0 (0.00%) | 0 (0.00%) | 2 (0.00%) | 2 (0.00%) | 0 (0.00%) | 2 (0.00%) |
antisense | 191,551 (0.52%) | 204,790 (0.53%) | 178,062 (0.50%) | 205,243 (0.50%) | 201,319 (0.54%) | 189,642 (0.55%) |
known_ncrna | 0 (0.00%) | 0 (0.00%) | 1 (0.00%) | 0 (0.00%) | 1 (0.00%) | 1 (0.00%) |
lincRNA | 738,731 (2.00%) | 761,611 (1.97%) | 706,213 (1.98%) | 702,871 (1.71%) | 742,207 (1.99%) | 702,377 (2.03%) |
miRNA | 2479 (0.01%) | 2557 (0.01%) | 3497 (0.01%) | 3299 (0.01%) | 1525 (0.00%) | 1430 (0.00%) |
misc_RNA | 1,612,667 (4.37%) | 1,593,547 (4.12%) | 1,627,962 (4.57%) | 1,960,500 (4.76%) | 1,343,420 (3.59%) | 1,244,791 (3.59%) |
non_coding | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) |
polymorphic_pseudogene | 319 (0.00%) | 355 (0.00%) | 320 (0.00%) | 369 (0.00%) | 333 (0.00%) | 312 (0.00%) |
processed_pseudogene | 10,437 (0.03%) | 10,705 (0.03%) | 9812 (0.03%) | 11,241 (0.03%) | 10,275 (0.03%) | 8946 (0.03%) |
processed_transcript | 196,988 (0.53%) | 213,355 (0.55%) | 194,373 (0.55%) | 229,395 (0.56%) | 203,313 (0.54%) | 192,191 (0.55%) |
protein_coding | 32,728,357 | 34,372,393 | 31,562,319 | 36,554,719 | 33,423,746 | 30,949,051 |
(88.74%) | (88.92%) | (88.65%) | (88.74%) | (89.42%) | (89.36%) | |
pseudogene | 147 (0.00%) | 166 (0.00%) | 145 (0.00%) | 153 (0.00%) | 172 (0.00%) | 167 (0.00%) |
rRNA | 32 (0.00%) | 44 (0.00%) | 38 (0.00%) | 62 (0.00%) | 46 (0.00%) | 44 (0.00%) |
sense_intronic | 1015 (0.00%) | 1032 (0.00%) | 1070 (0.00%) | 1071 (0.00%) | 1035 (0.00%) | 1021 (0.00%) |
sense_overlapping | 14,067 (0.04%) | 15,375 (0.04%) | 12,765 (0.04%) | 14,949 (0.04%) | 15,117 (0.04%) | 14,014 (0.04%) |
snRNA | 3417 (0.01%) | 3214 (0.01%) | 2915 (0.01%) | 3858 (0.01%) | 3149 (0.01%) | 3236 (0.01%) |
snoRNA | 160 (0.00%) | 172 (0.00%) | 136 (0.00%) | 149 (0.00%) | 197 (0.00%) | 170 (0.00%) |
transcribed_processed_pseudogene | 25,420 (0.07%) | 26,038 (0.07%) | 24,532 (0.07%) | 28,196 (0.07%) | 25,315 (0.07%) | 23,318 (0.07%) |
transcribed_unitary_pseudogene | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) |
transcribed_unprocessed_pseudogene | 72,052 (0.20%) | 77,671 (0.20%) | 69,487 (0.20%) | 79,027 (0.19%) | 78,124 (0.21%) | 73,283 (0.21%) |
translated_processed_pseudogene | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) |
translated_unprocessed_pseudogene | 1 (0.00%) | 0 (0.00%) | 0 (0.00%) | 1 (0.00%) | 0 (0.00%) | 0 (0.00%) |
unitary_pseudogene | 7892 (0.02%) | 8444 (0.02%) | 7147 (0.02%) | 8507 (0.02%) | 8233 (0.02%) | 7525 (0.02%) |
unprocessed_pseudogene | 12,070 (0.03%) | 12,228 (0.03%) | 11,432 (0.03%) | 12,660 (0.03%) | 12,177 (0.03%) | 11,856 (0.03%) |
Others | 1,257,539 (3.41%) | 1,342,963 (3.47%) | 1,185,376 (3.33%) | 1,370,001 (3.33%) | 1,299,971 (3.48%) | 1,201,876 (3.47%) |