{
    "Paralogy": {
        "lncRNA": {
            "1": 45469,
            "2": 752,
            "5": 138,
            "6": 55,
            "3": 196,
            "8": 24,
            "21": 1,
            "32": 3,
            "10": 30,
            "25": 1,
            "4": 165,
            "19": 24,
            "7": 42,
            "13": 14,
            "9": 65,
            "12": 7,
            "11": 25,
            "14": 10,
            "20": 13,
            "22": 2,
            "15": 2,
            "16": 2
        },
        "protein_coding": {
            "1": 84465,
            "2": 959,
            "3": 230,
            "5": 85,
            "7": 14,
            "6": 27,
            "4": 133,
            "10": 16,
            "8": 5,
            "11": 9,
            "9": 9,
            "12": 2
        },
        "processed_transcript": {
            "1": 27259,
            "2": 424,
            "4": 105,
            "7": 12,
            "3": 111,
            "5": 65,
            "8": 14,
            "6": 19,
            "13": 2,
            "12": 4,
            "10": 4,
            "9": 2
        },
        "nonsense_mediated_decay": {
            "1": 16128,
            "2": 151,
            "3": 36,
            "4": 34,
            "6": 12,
            "5": 37,
            "8": 3,
            "7": 4,
            "9": 2
        },
        "retained_intron": {
            "1": 28191,
            "2": 315,
            "7": 7,
            "5": 23,
            "6": 13,
            "3": 64,
            "4": 62,
            "8": 1,
            "9": 6,
            "10": 3,
            "14": 1
        },
        "processed_pseudogene": {
            "1": 9373,
            "2": 329,
            "11": 30,
            "4": 85,
            "6": 56,
            "3": 100,
            "14": 5,
            "12": 32,
            "13": 31,
            "7": 42,
            "5": 37,
            "8": 48,
            "9": 18,
            "15": 3,
            "10": 10
        },
        "misc_RNA": {
            "1": 2117,
            "2": 31,
            "6": 7,
            "5": 7,
            "7": 6,
            "4": 2,
            "9": 6,
            "3": 6
        },
        "TEC": {
            "1": 1146,
            "2": 57,
            "7": 12,
            "3": 11,
            "5": 9,
            "9": 9,
            "8": 9,
            "4": 8,
            "6": 3,
            "11": 9,
            "16": 5
        },
        "snoRNA": {
            "1": 918,
            "2": 8,
            "9": 6,
            "3": 3
        },
        "miRNA": {
            "1": 1816,
            "2": 45,
            "4": 10,
            "3": 6,
            "12": 24,
            "8": 13,
            "5": 2,
            "7": 5,
            "10": 1
        },
        "unprocessed_pseudogene": {
            "1": 1868,
            "2": 285,
            "5": 43,
            "4": 84,
            "3": 123,
            "11": 25,
            "7": 23,
            "8": 7,
            "6": 19,
            "10": 8,
            "9": 16,
            "14": 6,
            "12": 5,
            "15": 4,
            "13": 1,
            "16": 1
        },
        "snRNA": {
            "1": 1774,
            "2": 22,
            "4": 15,
            "5": 13,
            "3": 12,
            "6": 7,
            "9": 1
        },
        "transcribed_processed_pseudogene": {
            "1": 445,
            "2": 25,
            "8": 10,
            "5": 4,
            "4": 8,
            "9": 1,
            "6": 1,
            "3": 7,
            "10": 14,
            "7": 4
        },
        "transcribed_unprocessed_pseudogene": {
            "4": 28,
            "1": 686,
            "2": 149,
            "7": 7,
            "3": 44,
            "5": 27,
            "13": 2,
            "6": 10,
            "9": 2,
            "15": 6,
            "11": 2,
            "17": 1,
            "21": 1,
            "16": 2,
            "8": 4,
            "12": 2
        },
        "pseudogene": {
            "1": 28,
            "6": 1,
            "5": 1
        },
        "non_stop_decay": {
            "2": 1,
            "1": 89
        },
        "transcribed_unitary_pseudogene": {
            "1": 143,
            "2": 1
        },
        "rRNA_pseudogene": {
            "1": 468,
            "2": 5,
            "4": 9,
            "10": 4,
            "9": 1,
            "3": 1
        },
        "IG_V_pseudogene": {
            "11": 13,
            "1": 89,
            "3": 6,
            "2": 36,
            "4": 6
        },
        "IG_V_gene": {
            "1": 60,
            "2": 20,
            "4": 4,
            "3": 8
        },
        "scaRNA": {
            "1": 48
        },
        "StringTie": {
            "1": 48,
            "2": 4,
            "14": 2,
            "4": 1,
            "23": 1
        },
        "unitary_pseudogene": {
            "1": 91,
            "2": 2
        },
        "polymorphic_pseudogene": {
            "1": 80,
            "6": 1
        },
        "rRNA": {
            "1": 97,
            "2": 1,
            "10": 1,
            "5": 2
        },
        "ribozyme": {
            "1": 8
        },
        "Mt_tRNA": {
            "1": 2
        },
        "TR_V_gene": {
            "1": 85,
            "3": 10,
            "2": 8
        },
        "TR_V_pseudogene": {
            "1": 28,
            "3": 1,
            "4": 2,
            "2": 2
        },
        "vault_RNA": {
            "1": 1
        },
        "sRNA": {
            "1": 5
        },
        "IG_J_gene": {
            "1": 13
        },
        "IG_C_gene": {
            "1": 16
        },
        "IG_C_pseudogene": {
            "1": 7
        },
        "IG_D_gene": {
            "2": 2,
            "1": 4
        },
        "IG_J_pseudogene": {
            "1": 1
        },
        "IG_pseudogene": {
            "1": 1
        },
        "scRNA": {
            "1": 2
        },
        "translated_unprocessed_pseudogene": {
            "3": 1
        },
        "TR_J_gene": {
            "1": 64,
            "2": 2
        },
        "TR_C_gene": {
            "1": 4,
            "2": 2
        },
        "unknown_likely_coding": {
            "1": 12,
            "2": 2
        },
        "Mt_rRNA": {
            "1": 1
        },
        "TR_J_pseudogene": {
            "1": 4
        },
        "translated_processed_pseudogene": {
            "1": 1
        }
    },
    "UnfilteredParalogy": {
        "lncRNA": {
            "1": 44911,
            "2": 977,
            "8": 57,
            "6": 61,
            "3": 295,
            "32": 2,
            "10": 37,
            "5": 155,
            "42": 1,
            "9": 42,
            "40": 1,
            "4": 210,
            "14": 23,
            "7": 83,
            "12": 12,
            "13": 25,
            "11": 39,
            "16": 8,
            "22": 24,
            "21": 8,
            "15": 27,
            "18": 11,
            "33": 5,
            "19": 20,
            "38": 1,
            "25": 1,
            "17": 2,
            "20": 2
        },
        "protein_coding": {
            "1": 83628,
            "2": 1381,
            "5": 107,
            "3": 399,
            "7": 53,
            "4": 196,
            "6": 57,
            "8": 33,
            "28": 1,
            "16": 13,
            "12": 13,
            "9": 18,
            "10": 17,
            "33": 3,
            "32": 2,
            "17": 4,
            "13": 11,
            "15": 4,
            "11": 5,
            "21": 3,
            "20": 3,
            "18": 3
        },
        "processed_transcript": {
            "1": 26971,
            "2": 579,
            "4": 121,
            "3": 139,
            "7": 26,
            "5": 80,
            "6": 25,
            "13": 14,
            "17": 4,
            "9": 1,
            "8": 21,
            "14": 6,
            "10": 6,
            "16": 7,
            "23": 1,
            "33": 4,
            "12": 3,
            "20": 1,
            "39": 1,
            "38": 1,
            "11": 2,
            "15": 5,
            "21": 1,
            "22": 2
        },
        "nonsense_mediated_decay": {
            "1": 15951,
            "2": 237,
            "5": 36,
            "3": 69,
            "8": 13,
            "6": 14,
            "4": 45,
            "13": 5,
            "14": 4,
            "7": 23,
            "12": 1,
            "10": 3,
            "16": 4,
            "15": 1,
            "17": 1
        },
        "retained_intron": {
            "1": 28016,
            "2": 433,
            "7": 16,
            "3": 85,
            "5": 37,
            "6": 16,
            "13": 3,
            "9": 5,
            "4": 55,
            "8": 10,
            "10": 6,
            "14": 1,
            "16": 1,
            "11": 1,
            "17": 1
        },
        "processed_pseudogene": {
            "1": 9343,
            "2": 341,
            "11": 24,
            "4": 81,
            "6": 57,
            "3": 105,
            "14": 5,
            "12": 38,
            "13": 31,
            "7": 27,
            "5": 42,
            "8": 60,
            "9": 21,
            "10": 20,
            "15": 3,
            "20": 1
        },
        "misc_RNA": {
            "1": 2116,
            "2": 32,
            "6": 6,
            "5": 7,
            "7": 7,
            "4": 2,
            "9": 6,
            "3": 6
        },
        "TEC": {
            "1": 1137,
            "2": 61,
            "8": 10,
            "7": 10,
            "3": 12,
            "5": 10,
            "9": 12,
            "4": 9,
            "6": 3,
            "11": 9,
            "22": 2,
            "20": 3
        },
        "snoRNA": {
            "1": 918,
            "2": 8,
            "9": 6,
            "3": 3
        },
        "miRNA": {
            "1": 1816,
            "2": 45,
            "4": 10,
            "3": 6,
            "12": 24,
            "8": 13,
            "5": 2,
            "7": 5,
            "10": 1
        },
        "unprocessed_pseudogene": {
            "1": 1802,
            "2": 274,
            "3": 140,
            "5": 54,
            "4": 88,
            "7": 33,
            "12": 17,
            "19": 3,
            "8": 16,
            "10": 9,
            "6": 29,
            "9": 15,
            "14": 11,
            "13": 7,
            "15": 8,
            "11": 7,
            "17": 3,
            "16": 1,
            "22": 1
        },
        "snRNA": {
            "1": 1774,
            "3": 15,
            "4": 15,
            "5": 14,
            "2": 18,
            "6": 7,
            "9": 1
        },
        "transcribed_processed_pseudogene": {
            "1": 436,
            "2": 26,
            "8": 10,
            "5": 4,
            "4": 11,
            "9": 2,
            "3": 10,
            "11": 4,
            "10": 10,
            "13": 2,
            "7": 4
        },
        "transcribed_unprocessed_pseudogene": {
            "5": 28,
            "1": 630,
            "2": 158,
            "7": 9,
            "4": 38,
            "3": 58,
            "13": 4,
            "15": 9,
            "9": 2,
            "6": 13,
            "8": 11,
            "33": 1,
            "22": 1,
            "21": 3,
            "41": 1,
            "16": 2,
            "19": 1,
            "14": 1,
            "17": 1,
            "18": 1,
            "23": 1
        },
        "pseudogene": {
            "1": 28,
            "6": 1,
            "5": 1
        },
        "non_stop_decay": {
            "2": 2,
            "1": 87,
            "3": 1
        },
        "transcribed_unitary_pseudogene": {
            "1": 143,
            "2": 1
        },
        "rRNA_pseudogene": {
            "1": 467,
            "2": 6,
            "4": 9,
            "10": 4,
            "9": 1,
            "3": 1
        },
        "IG_V_pseudogene": {
            "11": 13,
            "1": 89,
            "3": 5,
            "2": 36,
            "4": 7
        },
        "IG_V_gene": {
            "1": 58,
            "2": 20,
            "4": 4,
            "5": 1,
            "3": 9
        },
        "scaRNA": {
            "1": 48
        },
        "StringTie": {
            "1": 45,
            "2": 2,
            "14": 2,
            "13": 1,
            "6": 3,
            "23": 1,
            "3": 2
        },
        "unitary_pseudogene": {
            "1": 91,
            "2": 2
        },
        "polymorphic_pseudogene": {
            "1": 80,
            "7": 1
        },
        "rRNA": {
            "1": 91,
            "2": 7,
            "10": 1,
            "5": 2
        },
        "ribozyme": {
            "1": 8
        },
        "Mt_tRNA": {
            "1": 2
        },
        "TR_V_gene": {
            "1": 85,
            "3": 10,
            "2": 8
        },
        "TR_V_pseudogene": {
            "1": 26,
            "2": 4,
            "3": 1,
            "4": 2
        },
        "vault_RNA": {
            "1": 1
        },
        "sRNA": {
            "1": 5
        },
        "IG_J_gene": {
            "1": 13
        },
        "IG_C_gene": {
            "1": 16
        },
        "IG_C_pseudogene": {
            "1": 7
        },
        "IG_D_gene": {
            "2": 4,
            "1": 2
        },
        "IG_J_pseudogene": {
            "1": 1
        },
        "IG_pseudogene": {
            "1": 1
        },
        "scRNA": {
            "1": 2
        },
        "translated_unprocessed_pseudogene": {
            "3": 1
        },
        "TR_J_gene": {
            "1": 64,
            "2": 2
        },
        "TR_C_gene": {
            "1": 3,
            "2": 2,
            "3": 1
        },
        "unknown_likely_coding": {
            "1": 11,
            "5": 1,
            "2": 1,
            "14": 1
        },
        "Mt_rRNA": {
            "1": 1
        },
        "TR_J_pseudogene": {
            "1": 4
        },
        "translated_processed_pseudogene": {
            "1": 1
        }
    },
    "Gene Family Collapse": {
        "protein_coding": {
            "3": 338,
            "2": 496,
            "4": 32,
            "9": 2,
            "15": 2,
            "22": 1,
            "5": 9,
            "6": 3,
            "7": 2
        },
        "polymorphic_pseudogene": {
            "2": 2
        },
        "IG_V_gene": {
            "2": 7,
            "3": 4
        },
        "TR_V_gene": {
            "2": 1
        },
        "TR_C_gene": {
            "3": 1
        },
        "IG_C_gene": {
            "2": 1
        },
        "IG_D_gene": {
            "2": 1
        },
        "processed_pseudogene": {
            "2": 243,
            "4": 62,
            "3": 80,
            "7": 4,
            "6": 18,
            "5": 20,
            "11": 3,
            "8": 1,
            "10": 2
        },
        "lncRNA": {
            "3": 174,
            "2": 550,
            "5": 37,
            "4": 40,
            "6": 11,
            "8": 3,
            "9": 2,
            "12": 1,
            "7": 5,
            "15": 1,
            "17": 2,
            "10": 2,
            "26": 1,
            "42": 1
        },
        "transcribed_processed_pseudogene": {
            "2": 31,
            "3": 11,
            "4": 8,
            "7": 1,
            "10": 2,
            "5": 2
        },
        "unprocessed_pseudogene": {
            "2": 189,
            "3": 70,
            "4": 21,
            "7": 5,
            "6": 8,
            "5": 18,
            "8": 1,
            "10": 2
        },
        "snRNA": {
            "2": 36,
            "3": 7,
            "4": 10,
            "11": 2
        },
        "transcribed_unitary_pseudogene": {
            "2": 6,
            "3": 2,
            "5": 1
        },
        "snoRNA": {
            "2": 35,
            "5": 2,
            "4": 2,
            "3": 1
        },
        "TEC": {
            "2": 55,
            "3": 18,
            "4": 16,
            "11": 3,
            "8": 1,
            "5": 2,
            "10": 1
        },
        "scaRNA": {
            "2": 5
        },
        "misc_RNA": {
            "2": 24,
            "5": 4,
            "3": 9,
            "6": 4,
            "4": 2
        },
        "transcribed_unprocessed_pseudogene": {
            "2": 75,
            "5": 8,
            "3": 38,
            "7": 2,
            "6": 8,
            "4": 12,
            "15": 2,
            "13": 1,
            "8": 1
        },
        "rRNA_pseudogene": {
            "2": 4,
            "6": 1,
            "3": 3
        },
        "rRNA": {
            "6": 1,
            "2": 3,
            "3": 1,
            "27": 1
        },
        "IG_V_pseudogene": {
            "3": 6,
            "2": 16,
            "7": 2,
            "5": 2,
            "4": 2
        },
        "miRNA": {
            "2": 25,
            "3": 5,
            "10": 2,
            "4": 2
        },
        "StringTie": {
            "2": 7,
            "6": 1,
            "3": 1
        },
        "vault_RNA": {
            "2": 1
        },
        "unitary_pseudogene": {
            "2": 3
        },
        "ribozyme": {
            "2": 1
        }
    },
    "Split Genes": {
        "Number of contig split genes": 58,
        "Number of intra-contig split genes": 57
    }
}