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 (
    12, 13, 14, 29, 40, 45, 51, 52, 69, 78, 85, 
    93, 96, 293, 564, 608, 15, 30, 41, 46, 
    50, 53, 68, 70, 79, 92, 97, 294, 609, 16, 
    31, 38, 42, 47, 54, 71, 77, 80, 87, 91, 
    94, 98, 295, 17, 32, 43, 44, 48, 55, 72, 
    81, 84, 88, 95, 99, 296, 597, 605, 18, 
    33, 49, 56, 73, 82, 83, 89, 297, 555, 607, 
    19, 34, 57, 74, 90, 298, 582, 600, 20, 
    35, 58, 75, 205, 604, 21, 37, 59, 76, 601, 
    22, 60, 23, 66, 24, 613, 25, 26, 27, 28, 
    36
  ) 
  AND companies.status = 'A' 
  AND products.company_id = 34 
  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 = 34 
  AND q_product_features.feature_type IN ('S', 'M', 'E') 
GROUP BY 
  q_product_features_values.variant_id

Query time 0.02035

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "973.81"
    },
    "grouping_operation": {
      "using_temporary_table": true,
      "using_filesort": true,
      "cost_info": {
        "sort_cost": "25.64"
      },
      "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": {
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            },
            "used_columns": [
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              "feature_type"
            ]
          }
        },
        {
          "table": {
            "table_name": "companies",
            "access_type": "const",
            "possible_keys": [
              "PRIMARY"
            ],
            "key": "PRIMARY",
            "used_key_parts": [
              "company_id"
            ],
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            "ref": [
              "const"
            ],
            "rows_examined_per_scan": 1,
            "rows_produced_per_join": 1,
            "filtered": "100.00",
            "cost_info": {
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            },
            "used_columns": [
              "company_id",
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            ]
          }
        },
        {
          "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": 2754,
            "rows_produced_per_join": 1377,
            "filtered": "100.00",
            "using_index": true,
            "using_join_buffer": "Block Nested Loop",
            "cost_info": {
              "read_cost": "310.32",
              "eval_cost": "275.40",
              "prefix_cost": "586.92",
              "data_read_per_join": "21K"
            },
            "used_columns": [
              "product_id",
              "category_id"
            ],
            "attached_condition": "(`portal`.`products_categories`.`category_id` in (12,13,14,29,40,45,51,52,69,78,85,93,96,293,564,608,15,30,41,46,50,53,68,70,79,92,97,294,609,16,31,38,42,47,54,71,77,80,87,91,94,98,295,17,32,43,44,48,55,72,81,84,88,95,99,296,597,605,18,33,49,56,73,82,83,89,297,555,607,19,34,57,74,90,298,582,600,20,35,58,75,205,604,21,37,59,76,601,22,60,23,66,24,613,25,26,27,28,36))"
          }
        },
        {
          "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": 275,
            "filtered": "20.00",
            "cost_info": {
              "read_cost": "0.00",
              "eval_cost": "55.08",
              "prefix_cost": "862.32",
              "data_read_per_join": "727K"
            },
            "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": 25,
            "filtered": "9.31",
            "cost_info": {
              "read_cost": "0.00",
              "eval_cost": "5.13",
              "prefix_cost": "917.40",
              "data_read_per_join": "151K"
            },
            "used_columns": [
              "product_id",
              "status",
              "company_id",
              "amount",
              "usergroup_ids",
              "tracking"
            ],
            "attached_condition": "((`portal`.`products`.`company_id` = 34) 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": 25,
            "filtered": "100.00",
            "cost_info": {
              "read_cost": "25.64",
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              "prefix_cost": "948.17",
              "data_read_per_join": "19K"
            },
            "used_columns": [
              "feature_id",
              "product_id",
              "variant_id",
              "lang_code"
            ]
          }
        }
      ]
    }
  }
}