diff --git a/compact.go b/compact.go
index 955ba3caf..28aefdd5b 100644
--- a/compact.go
+++ b/compact.go
@@ -525,22 +525,24 @@ func (c *LeveledCompactor) populateBlock(blocks []BlockReader, meta *BlockMeta,
 
 		if len(dranges) > 0 {
 			// Re-encode the chunk to not have deleted values.
-			for _, chk := range chks {
-				if intervalOverlap(dranges[0].Mint, dranges[len(dranges)-1].Maxt, chk.MinTime, chk.MaxTime) {
-					newChunk := chunks.NewXORChunk()
-					app, err := newChunk.Appender()
-					if err != nil {
-						return err
-					}
-
-					it := &deletedIterator{it: chk.Chunk.Iterator(), intervals: dranges}
-					for it.Next() {
-						ts, v := it.At()
-						app.Append(ts, v)
-					}
-
-					chk.Chunk = newChunk
+			for i, chk := range chks {
+				if !intervalOverlap(dranges[0].Mint, dranges[len(dranges)-1].Maxt, chk.MinTime, chk.MaxTime) {
+					continue
 				}
+
+				newChunk := chunks.NewXORChunk()
+				app, err := newChunk.Appender()
+				if err != nil {
+					return err
+				}
+
+				it := &deletedIterator{it: chk.Chunk.Iterator(), intervals: dranges}
+				for it.Next() {
+					ts, v := it.At()
+					app.Append(ts, v)
+				}
+
+				chks[i].Chunk = newChunk
 			}
 		}
 		if err := chunkw.WriteChunks(chks...); err != nil {
diff --git a/db.go b/db.go
index f1972f00b..1a500b244 100644
--- a/db.go
+++ b/db.go
@@ -612,7 +612,7 @@ func (db *DB) Snapshot(dir string) error {
 		level.Info(db.logger).Log("msg", "snapshotting block", "block", b)
 
 		if err := b.Snapshot(dir); err != nil {
-			return errors.Wrap(err, "error snapshotting headblock")
+			return errors.Wrapf(err, "error snapshotting block: %s", b.Dir())
 		}
 	}
 	return db.compactor.Write(dir, db.head, db.head.MinTime(), db.head.MaxTime())
diff --git a/db_test.go b/db_test.go
index 9f91705e7..fa8132290 100644
--- a/db_test.go
+++ b/db_test.go
@@ -366,6 +366,90 @@ func TestDB_Snapshot(t *testing.T) {
 	require.Equal(t, sum, 1000.0)
 }
 
+func TestDB_SnapshotWithDelete(t *testing.T) {
+	numSamples := int64(10)
+
+	db, close := openTestDB(t, nil)
+	defer close()
+
+	app := db.Appender()
+
+	smpls := make([]float64, numSamples)
+	for i := int64(0); i < numSamples; i++ {
+		smpls[i] = rand.Float64()
+		app.Add(labels.Labels{{"a", "b"}}, i, smpls[i])
+	}
+
+	require.NoError(t, app.Commit())
+	cases := []struct {
+		intervals Intervals
+		remaint   []int64
+	}{
+		{
+			intervals: Intervals{{1, 3}, {4, 7}},
+			remaint:   []int64{0, 8, 9},
+		},
+	}
+
+Outer:
+	for _, c := range cases {
+		// TODO(gouthamve): Reset the tombstones somehow.
+		// Delete the ranges.
+		for _, r := range c.intervals {
+			require.NoError(t, db.Delete(r.Mint, r.Maxt, labels.NewEqualMatcher("a", "b")))
+		}
+
+		// create snapshot
+		snap, err := ioutil.TempDir("", "snap")
+		require.NoError(t, err)
+		require.NoError(t, db.Snapshot(snap))
+		require.NoError(t, db.Close())
+
+		// reopen DB from snapshot
+		db, err = Open(snap, nil, nil, nil)
+		require.NoError(t, err)
+
+		// Compare the result.
+		q, err := db.Querier(0, numSamples)
+		require.NoError(t, err)
+
+		res := q.Select(labels.NewEqualMatcher("a", "b"))
+
+		expSamples := make([]sample, 0, len(c.remaint))
+		for _, ts := range c.remaint {
+			expSamples = append(expSamples, sample{ts, smpls[ts]})
+		}
+
+		expss := newListSeriesSet([]Series{
+			newSeries(map[string]string{"a": "b"}, expSamples),
+		})
+
+		if len(expSamples) == 0 {
+			require.False(t, res.Next())
+			continue
+		}
+
+		for {
+			eok, rok := expss.Next(), res.Next()
+			require.Equal(t, eok, rok, "next")
+
+			if !eok {
+				continue Outer
+			}
+			sexp := expss.At()
+			sres := res.At()
+
+			require.Equal(t, sexp.Labels(), sres.Labels(), "labels")
+
+			smplExp, errExp := expandSeriesIterator(sexp.Iterator())
+			smplRes, errRes := expandSeriesIterator(sres.Iterator())
+
+			require.Equal(t, errExp, errRes, "samples error")
+			require.Equal(t, smplExp, smplRes, "samples")
+		}
+	}
+}
+
 func TestDB_e2e(t *testing.T) {
 	const (
 		numDatapoints = 1000