SELECT 
  q_product_filters.filter_id, 
  q_product_features_values.variant_id 
FROM 
  q_product_features_values 
  LEFT JOIN q_products as products ON products.product_id = q_product_features_values.product_id 
  LEFT JOIN q_product_filters ON q_product_filters.feature_id = q_product_features_values.feature_id 
  LEFT JOIN q_product_features ON q_product_features.feature_id = q_product_features_values.feature_id 
  LEFT JOIN q_product_options_inventory as inventory ON inventory.product_id = products.product_id 
  LEFT JOIN q_companies AS companies ON companies.company_id = products.company_id 
  INNER JOIN q_products_categories as products_categories ON products_categories.product_id = products.product_id 
  INNER JOIN q_categories ON q_categories.category_id = products_categories.category_id 
  AND (
    q_categories.usergroup_ids = '' 
    OR FIND_IN_SET(0, q_categories.usergroup_ids) 
    OR FIND_IN_SET(1, q_categories.usergroup_ids)
  ) 
  AND q_categories.status IN ('A', 'H') 
WHERE 
  q_product_filters.filter_id IN (1, 3) 
  AND q_product_features_values.feature_id IN (2) 
  AND q_product_features_values.lang_code = 'en' 
  AND q_categories.category_id IN (
    248, 
    249, 
    250, 
    258, 
    259, 
    265, 
    274, 
    279, 
    280, 
    285, 
    303, 
    304, 
    316, 
    324, 
    331, 
    332, 
    345, 
    353, 
    362, 
    396, 
    435, 
    436, 
    490, 
    496, 
    500, 
    506, 
    545, 
    251, 
    257, 
    260, 
    264, 
    266, 
    275, 
    281, 
    284, 
    286, 
    305, 
    317, 
    325, 
    330, 
    333, 
    344, 
    346, 
    354, 
    363, 
    397, 
    492, 
    497, 
    501, 
    507, 
    546, 
    252, 
    261, 
    267, 
    273, 
    276, 
    282, 
    287, 
    288, 
    306, 
    318, 
    326, 
    334, 
    347, 
    352, 
    355, 
    364, 
    398, 
    498, 
    502, 
    508, 
    510, 
    547, 
    253, 
    262, 
    268, 
    277, 
    278, 
    283, 
    289, 
    307, 
    319, 
    327, 
    335, 
    348, 
    356, 
    365, 
    399, 
    499, 
    503, 
    509, 
    511, 
    548, 
    254, 
    263, 
    269, 
    290, 
    302, 
    308, 
    309, 
    320, 
    328, 
    336, 
    349, 
    357, 
    391, 
    489, 
    504, 
    255, 
    270, 
    291, 
    310, 
    315, 
    321, 
    329, 
    337, 
    350, 
    361, 
    392, 
    505, 
    532, 
    256, 
    272, 
    311, 
    322, 
    323, 
    338, 
    351, 
    358, 
    393, 
    271, 
    312, 
    339, 
    359, 
    395, 
    313, 
    340, 
    433, 
    544, 
    314, 
    341, 
    434, 
    566, 
    342, 
    343, 
    459, 
    569, 
    394, 
    598, 
    484, 
    533, 
    535, 
    579, 
    595
  ) 
  AND companies.status = 'A' 
  AND products.company_id = 28 
  AND (
    CASE products.tracking WHEN 'O' THEN inventory.amount > 0 WHEN 'B' THEN products.amount > 0 ELSE 1 END
  ) 
  AND (
    products.usergroup_ids = '' 
    OR FIND_IN_SET(0, products.usergroup_ids) 
    OR FIND_IN_SET(1, products.usergroup_ids)
  ) 
  AND products.status IN ('A') 
  AND products.company_id = 28 
  AND q_product_features.feature_type IN ('S', 'M', 'E') 
GROUP BY 
  q_product_features_values.variant_id

Query time 0.01601

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "527.28"
    },
    "grouping_operation": {
      "using_temporary_table": true,
      "using_filesort": true,
      "cost_info": {
        "sort_cost": "13.86"
      },
      "nested_loop": [
        {
          "table": {
            "table_name": "inventory",
            "access_type": "system",
            "possible_keys": [
              "pc"
            ],
            "rows_examined_per_scan": 0,
            "rows_produced_per_join": 1,
            "filtered": "0.00",
            "const_row_not_found": true,
            "cost_info": {
              "read_cost": "0.00",
              "eval_cost": "0.20",
              "prefix_cost": "0.00",
              "data_read_per_join": "976"
            },
            "used_columns": [
              "product_id",
              "amount"
            ]
          }
        },
        {
          "table": {
            "table_name": "q_product_features",
            "access_type": "const",
            "possible_keys": [
              "PRIMARY"
            ],
            "key": "PRIMARY",
            "used_key_parts": [
              "feature_id"
            ],
            "key_length": "3",
            "ref": [
              "const"
            ],
            "rows_examined_per_scan": 1,
            "rows_produced_per_join": 1,
            "filtered": "100.00",
            "cost_info": {
              "read_cost": "0.00",
              "eval_cost": "0.20",
              "prefix_cost": "0.00",
              "data_read_per_join": "432"
            },
            "used_columns": [
              "feature_id",
              "feature_type"
            ]
          }
        },
        {
          "table": {
            "table_name": "companies",
            "access_type": "const",
            "possible_keys": [
              "PRIMARY"
            ],
            "key": "PRIMARY",
            "used_key_parts": [
              "company_id"
            ],
            "key_length": "4",
            "ref": [
              "const"
            ],
            "rows_examined_per_scan": 1,
            "rows_produced_per_join": 1,
            "filtered": "100.00",
            "cost_info": {
              "read_cost": "0.00",
              "eval_cost": "0.20",
              "prefix_cost": "0.00",
              "data_read_per_join": "5K"
            },
            "used_columns": [
              "company_id",
              "status"
            ]
          }
        },
        {
          "table": {
            "table_name": "q_product_filters",
            "access_type": "ref",
            "possible_keys": [
              "PRIMARY",
              "feature_id"
            ],
            "key": "feature_id",
            "used_key_parts": [
              "feature_id"
            ],
            "key_length": "3",
            "ref": [
              "const"
            ],
            "rows_examined_per_scan": 1,
            "rows_produced_per_join": 0,
            "filtered": "50.00",
            "cost_info": {
              "read_cost": "1.00",
              "eval_cost": "0.10",
              "prefix_cost": "1.20",
              "data_read_per_join": "32"
            },
            "used_columns": [
              "filter_id",
              "feature_id"
            ],
            "attached_condition": "(`portal`.`q_product_filters`.`filter_id` in (1,3))"
          }
        },
        {
          "table": {
            "table_name": "products_categories",
            "access_type": "range",
            "possible_keys": [
              "PRIMARY",
              "pt"
            ],
            "key": "PRIMARY",
            "used_key_parts": [
              "category_id"
            ],
            "key_length": "3",
            "rows_examined_per_scan": 1489,
            "rows_produced_per_join": 744,
            "filtered": "100.00",
            "using_index": true,
            "using_join_buffer": "Block Nested Loop",
            "cost_info": {
              "read_cost": "168.00",
              "eval_cost": "148.90",
              "prefix_cost": "318.11",
              "data_read_per_join": "11K"
            },
            "used_columns": [
              "product_id",
              "category_id"
            ],
            "attached_condition": "(`portal`.`products_categories`.`category_id` in (248,249,250,258,259,265,274,279,280,285,303,304,316,324,331,332,345,353,362,396,435,436,490,496,500,506,545,251,257,260,264,266,275,281,284,286,305,317,325,330,333,344,346,354,363,397,492,497,501,507,546,252,261,267,273,276,282,287,288,306,318,326,334,347,352,355,364,398,498,502,508,510,547,253,262,268,277,278,283,289,307,319,327,335,348,356,365,399,499,503,509,511,548,254,263,269,290,302,308,309,320,328,336,349,357,391,489,504,255,270,291,310,315,321,329,337,350,361,392,505,532,256,272,311,322,323,338,351,358,393,271,312,339,359,395,313,340,433,544,314,341,434,566,342,343,459,569,394,598,484,533,535,579,595))"
          }
        },
        {
          "table": {
            "table_name": "q_categories",
            "access_type": "eq_ref",
            "possible_keys": [
              "PRIMARY",
              "c_status",
              "p_category_id"
            ],
            "key": "PRIMARY",
            "used_key_parts": [
              "category_id"
            ],
            "key_length": "3",
            "ref": [
              "portal.products_categories.category_id"
            ],
            "rows_examined_per_scan": 1,
            "rows_produced_per_join": 148,
            "filtered": "20.00",
            "cost_info": {
              "read_cost": "0.00",
              "eval_cost": "29.78",
              "prefix_cost": "467.00",
              "data_read_per_join": "393K"
            },
            "used_columns": [
              "category_id",
              "usergroup_ids",
              "status"
            ],
            "attached_condition": "(((`portal`.`q_categories`.`usergroup_ids` = '') or find_in_set(0,`portal`.`q_categories`.`usergroup_ids`) or find_in_set(1,`portal`.`q_categories`.`usergroup_ids`)) and (`portal`.`q_categories`.`status` in ('A','H')))"
          }
        },
        {
          "table": {
            "table_name": "products",
            "access_type": "eq_ref",
            "possible_keys": [
              "PRIMARY",
              "status"
            ],
            "key": "PRIMARY",
            "used_key_parts": [
              "product_id"
            ],
            "key_length": "3",
            "ref": [
              "portal.products_categories.product_id"
            ],
            "rows_examined_per_scan": 1,
            "rows_produced_per_join": 13,
            "filtered": "9.31",
            "cost_info": {
              "read_cost": "0.00",
              "eval_cost": "2.77",
              "prefix_cost": "496.79",
              "data_read_per_join": "81K"
            },
            "used_columns": [
              "product_id",
              "status",
              "company_id",
              "amount",
              "usergroup_ids",
              "tracking"
            ],
            "attached_condition": "((`portal`.`products`.`company_id` = 28) and (case `portal`.`products`.`tracking` when 'O' then <cache>((NULL > 0)) when 'B' then (`portal`.`products`.`amount` > 0) else 1 end) and ((`portal`.`products`.`usergroup_ids` = '') or find_in_set(0,`portal`.`products`.`usergroup_ids`) or find_in_set(1,`portal`.`products`.`usergroup_ids`)) and (`portal`.`products`.`status` = 'A'))"
          }
        },
        {
          "table": {
            "table_name": "q_product_features_values",
            "access_type": "ref",
            "possible_keys": [
              "PRIMARY",
              "fl",
              "variant_id",
              "lang_code",
              "product_id",
              "fpl"
            ],
            "key": "fpl",
            "used_key_parts": [
              "feature_id",
              "product_id",
              "lang_code"
            ],
            "key_length": "12",
            "ref": [
              "const",
              "portal.products_categories.product_id",
              "const"
            ],
            "rows_examined_per_scan": 1,
            "rows_produced_per_join": 13,
            "filtered": "100.00",
            "cost_info": {
              "read_cost": "13.86",
              "eval_cost": "2.77",
              "prefix_cost": "513.42",
              "data_read_per_join": "10K"
            },
            "used_columns": [
              "feature_id",
              "product_id",
              "variant_id",
              "lang_code"
            ]
          }
        }
      ]
    }
  }
}

Result

filter_id variant_id
1 7659