diff --git a/intact/intact.py b/intact/intact.py
index d95268a..b8df09a 100644
--- a/intact/intact.py
+++ b/intact/intact.py
@@ -110,6 +110,9 @@ class HolisticInfo:
     blast_matched_qlen: int  = dataclasses.field(default=None) # number of query nucleotides matched to a known reference sequence
     blast_sseq_coverage: float  = dataclasses.field(default=None) # percentage of reference sequence covered by the query sequence
     blast_qseq_coverage: float  = dataclasses.field(default=None) # percentage of the query sequence covered by reference sequence
+    blast_sseq_orfs_coverage: float  = dataclasses.field(default=None) # percentage of the query sequence covered by reference sequence
+    orfs_start: int  = dataclasses.field(default=None) # start position of the region used for orfs coverage
+    orfs_end: int  = dataclasses.field(default=None) # end position of the region used for orfs coverage
     blast_n_conseqs: int  = dataclasses.field(default=None) # number of blast conseqs in the resulting match
 
 
@@ -867,6 +870,13 @@ def intact( working_dir,
             blast_matched_slen = blast_rows[0].slen if blast_rows else 1
             holistic.blast_sseq_coverage = aligned_reference_length / blast_matched_slen
 
+            holistic.orfs_start = min(forward_orfs, key=lambda e: e.start).start
+            holistic.orfs_end = max(forward_orfs, key=lambda e: e.end).end
+            clamp = lambda p: max(holistic.orfs_start, min(holistic.orfs_end, p))
+            aligned_reference_orfs_length = sum(abs(clamp(x.send + 1) - clamp(x.sstart)) for x in blast_rows)
+            blast_matched_orfs_slen = holistic.orfs_end - holistic.orfs_start
+            holistic.blast_sseq_orfs_coverage = aligned_reference_orfs_length / blast_matched_orfs_slen
+
             reverse_sequence = SeqRecord.SeqRecord(Seq.reverse_complement(sequence.seq),
                                                    id = sequence.id + " [REVERSED]",
                                                    name = sequence.name
diff --git a/tests/expected-results-large-csv/holistic.csv b/tests/expected-results-large-csv/holistic.csv
index 383c944..fc0954a 100644
--- a/tests/expected-results-large-csv/holistic.csv
+++ b/tests/expected-results-large-csv/holistic.csv
@@ -1,42 +1,42 @@
-seqid,qlen,hypermutation_probablility,inferred_subtype,blast_matched_qlen,blast_sseq_coverage,blast_qseq_coverage,blast_n_conseqs
-KX505501.1,1997,0.7087072014754221,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,1997,0.2498199403230785,1.2158237356034052,4
-MN691959,9493,0.19593905853945925,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9493,1.0816956477003807,1.1086063415148004,3
-MN692074,4178,0.36378645339477633,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,4178,0.5041670953801831,1.1728099569171853,4
-MN692145,9689,0.1661041079701131,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9689,1.1304660973351168,1.1271545051088863,3
-MN090335,9069,0.1754017863888554,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9069,0.9842576396748637,1.0603153600176425,3
-MN090376,8985,0.026007919521734202,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,8985,0.9784957300133759,1.0604340567612687,3
-MK115581.1,9495,0.6897199265079494,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9495,0.9870357032616525,1.0046340179041602,2
-MK115690.1,9689,0.05065930954004094,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9689,0.988167506945159,0.9949427185468056,2
-MK115571.1,9394,0.8012585672082311,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9394,0.9866241382858318,1.0113902490951672,2
-MK115514.1,9382,0.6458974386368621,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9382,0.9864183557979216,1.0173736943082499,2
-MK115488.1,9623,0.6511896911074662,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9623,1.0255170285008746,1.0325262392185388,6
-MK115030.1,9126,0.031598631869680704,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9126,0.9940323078506019,1.0655270655270654,3
-MK115498.1,9461,0.8339748776671196,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9461,0.9866241382858318,1.0080329774865235,2
-MK115211.1,9032,0.11689558806708,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9032,0.9950612202901533,1.0598981399468557,3
-MK115158.1,9143,0.002572269807584293,Ref.47_BF.ES.08.P1942.GQ372987,9143,0.9921577414295317,0.9699223449633599,1
-MK114705.1,9411,0.14449377496074622,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9411,1.0980553554892478,1.122622463075125,6
-MK114856.1,9477,1.0,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9477,1.0485646671468258,1.0812493405085997,4
-MK115009.1,9207,1.0,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9207,0.9965016977055252,1.0590854784403172,3
-MK115387.1,9136,0.5412311092694289,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9136,0.9796275336968824,1.040936952714536,2
-MK115491.1,9422,0.8951015182445495,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9422,1.003704084782385,1.0299299511780937,2
-MK116110.1,8967,0.07021438897893317,Ref.B.TH.90.BK132.AY173951,8967,0.9957759004001778,0.9972119995539199,3
-MK115527.1,9481,0.7689834393883834,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9481,0.986727029529787,1.0056956017297753,2
-MK114997.1,9055,0.054959132555391754,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9055,0.9784957300133759,1.0516841524019878,2
-MK115518.1,9537,0.6385326595592609,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9537,0.9847720958946393,0.9996854356715948,3
-MK115065.1,9214,0.033517722768753644,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9214,1.0080255170285009,1.069459518124593,6
-MK115464.1,9663,1.0,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9663,0.9838460746990431,0.9893407844354756,2
-MK115530.1,9544,0.5789377103398377,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9544,0.9866241382858318,0.9992665549036044,2
-MK115520.1,9589,0.5200353682902832,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9589,0.9787015125012861,0.987902805297737,3
-MK115503.1,9617,0.4263025132504157,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9617,0.9870357032616525,0.9953207861079338,2
-MK115570.1,9485,0.738578434638724,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9485,0.9866241382858318,1.0057986294148655,2
-MK115509.1,9353,0.7866198309713798,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9353,0.9866241382858318,1.0197797498128942,2
-MK115702.1,9098,0.14401391767451666,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9098,0.987447268237473,1.0596834469114091,4
-MK115095.1,9137,1.0,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9137,0.9907397880440375,1.060085367188355,2
-MK115490.1,9347,0.8863248655310947,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9347,0.9848749871385946,1.0204343639670483,3
-MK115576.1,9266,0.818189227062389,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9266,0.9917687004835889,1.0342110943233327,3
-OQ092466,9686,0.3876036547663967,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9686,1.1015536577837226,1.1192442700805285,3
-OQ092463,9605,0.21628713708846803,Ref.B.TH.90.BK132.AY173951,9605,1.0529124055135617,0.9884435190005205,2
-OQ092465,9659,0.02412789935966586,Ref.28_BF.BR.99.BREPM12817.DQ085874,9659,1.0429696287964005,0.9620043482762191,2
-OQ092462,9714,0.10777665573070194,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9714,1.130671879823027,1.1301214741610048,3
-OQ092464,9556,0.006887768010151674,Ref.28_BF.BR.99.BREPM12817.DQ085874,9556,1.0427446569178853,0.9678735872750105,2
-OQ092467,9936,0.6416537859942263,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9936,1.1308776623109373,1.0962157809983897,3
+seqid,qlen,hypermutation_probablility,inferred_subtype,blast_matched_qlen,blast_sseq_coverage,blast_qseq_coverage,blast_sseq_orfs_coverage,orfs_start,orfs_end,blast_n_conseqs
+KX505501.1,1997,0.7087072014754221,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,1997,0.2498199403230785,1.2158237356034052,0.17661753684736448,789,8795,4
+MN691959,9493,0.19593905853945925,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9493,1.0816956477003807,1.1086063415148004,1.0,789,8795,3
+MN692074,4178,0.36378645339477633,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,4178,0.5041670953801831,1.1728099569171853,0.41144141893579816,789,8795,4
+MN692145,9689,0.1661041079701131,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9689,1.1304660973351168,1.1271545051088863,1.0,789,8795,3
+MN090335,9069,0.1754017863888554,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9069,0.9842576396748637,1.0603153600176425,1.0003747189607795,789,8795,3
+MN090376,8985,0.026007919521734202,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,8985,0.9784957300133759,1.0604340567612687,0.9943792155883088,789,8795,3
+MK115581.1,9495,0.6897199265079494,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9495,0.9870357032616525,1.0046340179041602,1.0,789,8795,2
+MK115690.1,9689,0.05065930954004094,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9689,0.988167506945159,0.9949427185468056,1.0,789,8795,2
+MK115571.1,9394,0.8012585672082311,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9394,0.9866241382858318,1.0113902490951672,1.0,789,8795,2
+MK115514.1,9382,0.6458974386368621,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9382,0.9864183557979216,1.0173736943082499,1.0,789,8795,2
+MK115488.1,9623,0.6511896911074662,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9623,1.0255170285008746,1.0325262392185388,1.0,789,8795,6
+MK115030.1,9126,0.031598631869680704,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9126,0.9940323078506019,1.0655270655270654,1.0,789,8795,3
+MK115498.1,9461,0.8339748776671196,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9461,0.9866241382858318,1.0080329774865235,1.0,789,8795,2
+MK115211.1,9032,0.11689558806708,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9032,0.9950612202901533,1.0598981399468557,1.0,789,8795,3
+MK115158.1,9143,0.002572269807584293,Ref.47_BF.ES.08.P1942.GQ372987,9143,0.9921577414295317,0.9699223449633599,1.0,234,8212,1
+MK114705.1,9411,0.14449377496074622,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9411,1.0980553554892478,1.122622463075125,1.0,789,8795,6
+MK114856.1,9477,1.0,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9477,1.0485646671468258,1.0812493405085997,1.0,789,8795,4
+MK115009.1,9207,1.0,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9207,0.9965016977055252,1.0590854784403172,1.0,789,8795,3
+MK115387.1,9136,0.5412311092694289,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9136,0.9796275336968824,1.040936952714536,1.0,789,8795,2
+MK115491.1,9422,0.8951015182445495,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9422,1.003704084782385,1.0299299511780937,1.0,789,8795,2
+MK116110.1,8967,0.07021438897893317,Ref.B.TH.90.BK132.AY173951,8967,0.9957759004001778,0.9972119995539199,0.998622244488978,140,8124,3
+MK115527.1,9481,0.7689834393883834,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9481,0.986727029529787,1.0056956017297753,1.0,789,8795,2
+MK114997.1,9055,0.054959132555391754,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9055,0.9784957300133759,1.0516841524019878,1.0,789,8795,2
+MK115518.1,9537,0.6385326595592609,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9537,0.9847720958946393,0.9996854356715948,1.0,789,8795,3
+MK115065.1,9214,0.033517722768753644,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9214,1.0080255170285009,1.069459518124593,1.0,789,8795,6
+MK115464.1,9663,1.0,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9663,0.9838460746990431,0.9893407844354756,1.0,789,8795,2
+MK115530.1,9544,0.5789377103398377,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9544,0.9866241382858318,0.9992665549036044,1.0,789,8795,2
+MK115520.1,9589,0.5200353682902832,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9589,0.9787015125012861,0.987902805297737,1.012115913065201,789,8795,3
+MK115503.1,9617,0.4263025132504157,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9617,0.9870357032616525,0.9953207861079338,1.0,789,8795,2
+MK115570.1,9485,0.738578434638724,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9485,0.9866241382858318,1.0057986294148655,1.0,789,8795,2
+MK115509.1,9353,0.7866198309713798,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9353,0.9866241382858318,1.0197797498128942,1.0,789,8795,2
+MK115702.1,9098,0.14401391767451666,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9098,0.987447268237473,1.0596834469114091,1.019860104921309,789,8795,4
+MK115095.1,9137,1.0,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9137,0.9907397880440375,1.060085367188355,1.0,789,8795,2
+MK115490.1,9347,0.8863248655310947,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9347,0.9848749871385946,1.0204343639670483,1.0,789,8795,3
+MK115576.1,9266,0.818189227062389,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9266,0.9917687004835889,1.0342110943233327,1.0,789,8795,3
+OQ092466,9686,0.3876036547663967,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9686,1.1015536577837226,1.1192442700805285,1.0,789,8795,3
+OQ092463,9605,0.21628713708846803,Ref.B.TH.90.BK132.AY173951,9605,1.0529124055135617,0.9884435190005205,1.0,140,8124,2
+OQ092465,9659,0.02412789935966586,Ref.28_BF.BR.99.BREPM12817.DQ085874,9659,1.0429696287964005,0.9620043482762191,1.0,200,8208,2
+OQ092462,9714,0.10777665573070194,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9714,1.130671879823027,1.1301214741610048,1.0,789,8795,3
+OQ092464,9556,0.006887768010151674,Ref.28_BF.BR.99.BREPM12817.DQ085874,9556,1.0427446569178853,0.9678735872750105,1.0,200,8208,2
+OQ092467,9936,0.6416537859942263,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9936,1.1308776623109373,1.0962157809983897,1.0,789,8795,3
diff --git a/tests/expected-results-large/holistic.json b/tests/expected-results-large/holistic.json
index f98371a..a84c4dc 100644
--- a/tests/expected-results-large/holistic.json
+++ b/tests/expected-results-large/holistic.json
@@ -6,6 +6,9 @@
         "blast_matched_qlen": 1997,
         "blast_sseq_coverage": 0.2498199403230785,
         "blast_qseq_coverage": 1.2158237356034052,
+        "blast_sseq_orfs_coverage": 0.17661753684736448,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 4
     },
     "MN691959": {
@@ -15,6 +18,9 @@
         "blast_matched_qlen": 9493,
         "blast_sseq_coverage": 1.0816956477003807,
         "blast_qseq_coverage": 1.1086063415148004,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 3
     },
     "MN692074": {
@@ -24,6 +30,9 @@
         "blast_matched_qlen": 4178,
         "blast_sseq_coverage": 0.5041670953801831,
         "blast_qseq_coverage": 1.1728099569171853,
+        "blast_sseq_orfs_coverage": 0.41144141893579816,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 4
     },
     "MN692145": {
@@ -33,6 +42,9 @@
         "blast_matched_qlen": 9689,
         "blast_sseq_coverage": 1.1304660973351168,
         "blast_qseq_coverage": 1.1271545051088863,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 3
     },
     "MN090335": {
@@ -42,6 +54,9 @@
         "blast_matched_qlen": 9069,
         "blast_sseq_coverage": 0.9842576396748637,
         "blast_qseq_coverage": 1.0603153600176425,
+        "blast_sseq_orfs_coverage": 1.0003747189607795,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 3
     },
     "MN090376": {
@@ -51,6 +66,9 @@
         "blast_matched_qlen": 8985,
         "blast_sseq_coverage": 0.9784957300133759,
         "blast_qseq_coverage": 1.0604340567612687,
+        "blast_sseq_orfs_coverage": 0.9943792155883088,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 3
     },
     "MK115581.1": {
@@ -60,6 +78,9 @@
         "blast_matched_qlen": 9495,
         "blast_sseq_coverage": 0.9870357032616525,
         "blast_qseq_coverage": 1.0046340179041602,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 2
     },
     "MK115690.1": {
@@ -69,6 +90,9 @@
         "blast_matched_qlen": 9689,
         "blast_sseq_coverage": 0.988167506945159,
         "blast_qseq_coverage": 0.9949427185468056,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 2
     },
     "MK115571.1": {
@@ -78,6 +102,9 @@
         "blast_matched_qlen": 9394,
         "blast_sseq_coverage": 0.9866241382858318,
         "blast_qseq_coverage": 1.0113902490951672,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 2
     },
     "MK115514.1": {
@@ -87,6 +114,9 @@
         "blast_matched_qlen": 9382,
         "blast_sseq_coverage": 0.9864183557979216,
         "blast_qseq_coverage": 1.0173736943082499,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 2
     },
     "MK115488.1": {
@@ -96,6 +126,9 @@
         "blast_matched_qlen": 9623,
         "blast_sseq_coverage": 1.0255170285008746,
         "blast_qseq_coverage": 1.0325262392185388,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 6
     },
     "MK115030.1": {
@@ -105,6 +138,9 @@
         "blast_matched_qlen": 9126,
         "blast_sseq_coverage": 0.9940323078506019,
         "blast_qseq_coverage": 1.0655270655270654,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 3
     },
     "MK115498.1": {
@@ -114,6 +150,9 @@
         "blast_matched_qlen": 9461,
         "blast_sseq_coverage": 0.9866241382858318,
         "blast_qseq_coverage": 1.0080329774865235,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 2
     },
     "MK115211.1": {
@@ -123,6 +162,9 @@
         "blast_matched_qlen": 9032,
         "blast_sseq_coverage": 0.9950612202901533,
         "blast_qseq_coverage": 1.0598981399468557,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 3
     },
     "MK115158.1": {
@@ -132,6 +174,9 @@
         "blast_matched_qlen": 9143,
         "blast_sseq_coverage": 0.9921577414295317,
         "blast_qseq_coverage": 0.9699223449633599,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 234,
+        "orfs_end": 8212,
         "blast_n_conseqs": 1
     },
     "MK114705.1": {
@@ -141,6 +186,9 @@
         "blast_matched_qlen": 9411,
         "blast_sseq_coverage": 1.0980553554892478,
         "blast_qseq_coverage": 1.122622463075125,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 6
     },
     "MK114856.1": {
@@ -150,6 +198,9 @@
         "blast_matched_qlen": 9477,
         "blast_sseq_coverage": 1.0485646671468258,
         "blast_qseq_coverage": 1.0812493405085997,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 4
     },
     "MK115009.1": {
@@ -159,6 +210,9 @@
         "blast_matched_qlen": 9207,
         "blast_sseq_coverage": 0.9965016977055252,
         "blast_qseq_coverage": 1.0590854784403172,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 3
     },
     "MK115387.1": {
@@ -168,6 +222,9 @@
         "blast_matched_qlen": 9136,
         "blast_sseq_coverage": 0.9796275336968824,
         "blast_qseq_coverage": 1.040936952714536,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 2
     },
     "MK115491.1": {
@@ -177,6 +234,9 @@
         "blast_matched_qlen": 9422,
         "blast_sseq_coverage": 1.003704084782385,
         "blast_qseq_coverage": 1.0299299511780937,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 2
     },
     "MK116110.1": {
@@ -186,6 +246,9 @@
         "blast_matched_qlen": 8967,
         "blast_sseq_coverage": 0.9957759004001778,
         "blast_qseq_coverage": 0.9972119995539199,
+        "blast_sseq_orfs_coverage": 0.998622244488978,
+        "orfs_start": 140,
+        "orfs_end": 8124,
         "blast_n_conseqs": 3
     },
     "MK115527.1": {
@@ -195,6 +258,9 @@
         "blast_matched_qlen": 9481,
         "blast_sseq_coverage": 0.986727029529787,
         "blast_qseq_coverage": 1.0056956017297753,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 2
     },
     "MK114997.1": {
@@ -204,6 +270,9 @@
         "blast_matched_qlen": 9055,
         "blast_sseq_coverage": 0.9784957300133759,
         "blast_qseq_coverage": 1.0516841524019878,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 2
     },
     "MK115518.1": {
@@ -213,6 +282,9 @@
         "blast_matched_qlen": 9537,
         "blast_sseq_coverage": 0.9847720958946393,
         "blast_qseq_coverage": 0.9996854356715948,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 3
     },
     "MK115065.1": {
@@ -222,6 +294,9 @@
         "blast_matched_qlen": 9214,
         "blast_sseq_coverage": 1.0080255170285009,
         "blast_qseq_coverage": 1.069459518124593,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 6
     },
     "MK115464.1": {
@@ -231,6 +306,9 @@
         "blast_matched_qlen": 9663,
         "blast_sseq_coverage": 0.9838460746990431,
         "blast_qseq_coverage": 0.9893407844354756,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 2
     },
     "MK115530.1": {
@@ -240,6 +318,9 @@
         "blast_matched_qlen": 9544,
         "blast_sseq_coverage": 0.9866241382858318,
         "blast_qseq_coverage": 0.9992665549036044,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 2
     },
     "MK115520.1": {
@@ -249,6 +330,9 @@
         "blast_matched_qlen": 9589,
         "blast_sseq_coverage": 0.9787015125012861,
         "blast_qseq_coverage": 0.987902805297737,
+        "blast_sseq_orfs_coverage": 1.012115913065201,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 3
     },
     "MK115503.1": {
@@ -258,6 +342,9 @@
         "blast_matched_qlen": 9617,
         "blast_sseq_coverage": 0.9870357032616525,
         "blast_qseq_coverage": 0.9953207861079338,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 2
     },
     "MK115570.1": {
@@ -267,6 +354,9 @@
         "blast_matched_qlen": 9485,
         "blast_sseq_coverage": 0.9866241382858318,
         "blast_qseq_coverage": 1.0057986294148655,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 2
     },
     "MK115509.1": {
@@ -276,6 +366,9 @@
         "blast_matched_qlen": 9353,
         "blast_sseq_coverage": 0.9866241382858318,
         "blast_qseq_coverage": 1.0197797498128942,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 2
     },
     "MK115702.1": {
@@ -285,6 +378,9 @@
         "blast_matched_qlen": 9098,
         "blast_sseq_coverage": 0.987447268237473,
         "blast_qseq_coverage": 1.0596834469114091,
+        "blast_sseq_orfs_coverage": 1.019860104921309,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 4
     },
     "MK115095.1": {
@@ -294,6 +390,9 @@
         "blast_matched_qlen": 9137,
         "blast_sseq_coverage": 0.9907397880440375,
         "blast_qseq_coverage": 1.060085367188355,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 2
     },
     "MK115490.1": {
@@ -303,6 +402,9 @@
         "blast_matched_qlen": 9347,
         "blast_sseq_coverage": 0.9848749871385946,
         "blast_qseq_coverage": 1.0204343639670483,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 3
     },
     "MK115576.1": {
@@ -312,6 +414,9 @@
         "blast_matched_qlen": 9266,
         "blast_sseq_coverage": 0.9917687004835889,
         "blast_qseq_coverage": 1.0342110943233327,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 3
     },
     "OQ092466": {
@@ -321,6 +426,9 @@
         "blast_matched_qlen": 9686,
         "blast_sseq_coverage": 1.1015536577837226,
         "blast_qseq_coverage": 1.1192442700805285,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 3
     },
     "OQ092463": {
@@ -330,6 +438,9 @@
         "blast_matched_qlen": 9605,
         "blast_sseq_coverage": 1.0529124055135617,
         "blast_qseq_coverage": 0.9884435190005205,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 140,
+        "orfs_end": 8124,
         "blast_n_conseqs": 2
     },
     "OQ092465": {
@@ -339,6 +450,9 @@
         "blast_matched_qlen": 9659,
         "blast_sseq_coverage": 1.0429696287964005,
         "blast_qseq_coverage": 0.9620043482762191,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 200,
+        "orfs_end": 8208,
         "blast_n_conseqs": 2
     },
     "OQ092462": {
@@ -348,6 +462,9 @@
         "blast_matched_qlen": 9714,
         "blast_sseq_coverage": 1.130671879823027,
         "blast_qseq_coverage": 1.1301214741610048,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 3
     },
     "OQ092464": {
@@ -357,6 +474,9 @@
         "blast_matched_qlen": 9556,
         "blast_sseq_coverage": 1.0427446569178853,
         "blast_qseq_coverage": 0.9678735872750105,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 200,
+        "orfs_end": 8208,
         "blast_n_conseqs": 2
     },
     "OQ092467": {
@@ -366,6 +486,9 @@
         "blast_matched_qlen": 9936,
         "blast_sseq_coverage": 1.1308776623109373,
         "blast_qseq_coverage": 1.0962157809983897,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 3
     }
 }
\ No newline at end of file
diff --git a/tests/expected-results-single-csv/holistic.csv b/tests/expected-results-single-csv/holistic.csv
index f1840a4..d3d8de7 100644
--- a/tests/expected-results-single-csv/holistic.csv
+++ b/tests/expected-results-single-csv/holistic.csv
@@ -1,2 +1,2 @@
-seqid,qlen,hypermutation_probablility,inferred_subtype,blast_matched_qlen,blast_sseq_coverage,blast_qseq_coverage,blast_n_conseqs
-MN692145,9689,0.1661041079701131,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9689,1.1304660973351168,1.1271545051088863,3
+seqid,qlen,hypermutation_probablility,inferred_subtype,blast_matched_qlen,blast_sseq_coverage,blast_qseq_coverage,blast_sseq_orfs_coverage,orfs_start,orfs_end,blast_n_conseqs
+MN692145,9689,0.1661041079701131,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9689,1.1304660973351168,1.1271545051088863,1.0,789,8795,3
diff --git a/tests/expected-results-single/holistic.json b/tests/expected-results-single/holistic.json
index 3cd930d..060aa5a 100644
--- a/tests/expected-results-single/holistic.json
+++ b/tests/expected-results-single/holistic.json
@@ -6,6 +6,9 @@
         "blast_matched_qlen": 9689,
         "blast_sseq_coverage": 1.1304660973351168,
         "blast_qseq_coverage": 1.1271545051088863,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 3
     }
 }
\ No newline at end of file
diff --git a/tests/expected-results-small-csv/holistic.csv b/tests/expected-results-small-csv/holistic.csv
index 8da1aa4..0dd3a51 100644
--- a/tests/expected-results-small-csv/holistic.csv
+++ b/tests/expected-results-small-csv/holistic.csv
@@ -1,6 +1,6 @@
-seqid,qlen,hypermutation_probablility,inferred_subtype,blast_matched_qlen,blast_sseq_coverage,blast_qseq_coverage,blast_n_conseqs
-KX505501.1,1997,0.7087072014754221,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,1997,0.2498199403230785,1.2158237356034052,4
-MN691959,9493,0.19593905853945925,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9493,1.0816956477003807,1.1086063415148004,3
-MN692074,4178,0.36378645339477633,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,4178,0.5041670953801831,1.1728099569171853,4
-MN692145,9689,0.1661041079701131,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9689,1.1304660973351168,1.1271545051088863,3
-MN090335,9069,0.1754017863888554,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9069,0.9842576396748637,1.0603153600176425,3
+seqid,qlen,hypermutation_probablility,inferred_subtype,blast_matched_qlen,blast_sseq_coverage,blast_qseq_coverage,blast_sseq_orfs_coverage,orfs_start,orfs_end,blast_n_conseqs
+KX505501.1,1997,0.7087072014754221,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,1997,0.2498199403230785,1.2158237356034052,0.17661753684736448,789,8795,4
+MN691959,9493,0.19593905853945925,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9493,1.0816956477003807,1.1086063415148004,1.0,789,8795,3
+MN692074,4178,0.36378645339477633,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,4178,0.5041670953801831,1.1728099569171853,0.41144141893579816,789,8795,4
+MN692145,9689,0.1661041079701131,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9689,1.1304660973351168,1.1271545051088863,1.0,789,8795,3
+MN090335,9069,0.1754017863888554,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,9069,0.9842576396748637,1.0603153600176425,1.0003747189607795,789,8795,3
diff --git a/tests/expected-results-small/holistic.json b/tests/expected-results-small/holistic.json
index 2bbd7d0..f80f6bf 100644
--- a/tests/expected-results-small/holistic.json
+++ b/tests/expected-results-small/holistic.json
@@ -6,6 +6,9 @@
         "blast_matched_qlen": 1997,
         "blast_sseq_coverage": 0.2498199403230785,
         "blast_qseq_coverage": 1.2158237356034052,
+        "blast_sseq_orfs_coverage": 0.17661753684736448,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 4
     },
     "MN691959": {
@@ -15,6 +18,9 @@
         "blast_matched_qlen": 9493,
         "blast_sseq_coverage": 1.0816956477003807,
         "blast_qseq_coverage": 1.1086063415148004,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 3
     },
     "MN692074": {
@@ -24,6 +30,9 @@
         "blast_matched_qlen": 4178,
         "blast_sseq_coverage": 0.5041670953801831,
         "blast_qseq_coverage": 1.1728099569171853,
+        "blast_sseq_orfs_coverage": 0.41144141893579816,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 4
     },
     "MN692145": {
@@ -33,6 +42,9 @@
         "blast_matched_qlen": 9689,
         "blast_sseq_coverage": 1.1304660973351168,
         "blast_qseq_coverage": 1.1271545051088863,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 3
     },
     "MN090335": {
@@ -42,6 +54,9 @@
         "blast_matched_qlen": 9069,
         "blast_sseq_coverage": 0.9842576396748637,
         "blast_qseq_coverage": 1.0603153600176425,
+        "blast_sseq_orfs_coverage": 1.0003747189607795,
+        "orfs_start": 789,
+        "orfs_end": 8795,
         "blast_n_conseqs": 3
     }
 }
\ No newline at end of file