# Summary statistics, used for scaling the plots.
SS	Number of files:	1
SS	Number of amplicons:	vir1	2
SS	Reference length:	vir1	800
SS	Number of amplicons:	vir2	3
SS	Reference length:	vir2	900
SS	End of summary
# Amplicon locations from BED file.
# LEFT/RIGHT are <start>-<end> format and comma-separated for alt-primers.
#
# AMPLICON	REF	NUMBER	LEFT	RIGHT
AMPLICON	vir1	1	31-54	386-410
AMPLICON	vir1	2	321-342	705-726
AMPLICON	vir2	3	11-35,21-40	301-330
AMPLICON	vir2	4	261-275	441-460
AMPLICON	vir2	5	401-420	851-880,856-882
# Summary stats.
# Use 'grep ^FSS | cut -f 2-' to extract this part.
FSS	mixed_clipped	vir1	raw total sequences:	8
FSS	mixed_clipped	vir1	filtered sequences:	0
FSS	mixed_clipped	vir1	failed primer match:	2
FSS	mixed_clipped	vir1	matching sequences:	6
FSS	mixed_clipped	vir1	consensus depth count < 1 and >= 1:	132	517
FSS	mixed_clipped	vir2	raw total sequences:	10
FSS	mixed_clipped	vir2	filtered sequences:	0
FSS	mixed_clipped	vir2	failed primer match:	0
FSS	mixed_clipped	vir2	matching sequences:	10
FSS	mixed_clipped	vir2	consensus depth count < 1 and >= 1:	140	669
# Absolute matching read counts per amplicon.
# Use 'grep ^FREADS | cut -f 2-' to extract this part.
FREADS	mixed_clipped	5	1	6	0	4
FVDEPTH	mixed_clipped	2	0	2	0	1
# Read percentage of distribution between amplicons.
# Use 'grep ^FRPERC | cut -f 2-' to extract this part.
FRPERC	mixed_clipped	31.250	6.250	37.500	0.000	25.000
# Read depth per amplicon.
# Use 'grep ^FDEPTH | cut -f 2-' to extract this part.
FDEPTH	mixed_clipped	2.8	0.5	3.9	0.0	1.7
# Percentage coverage per amplicon
# Use 'grep ^FPCOV | cut -f 2-' to extract this part.
FPCOV-1	mixed_clipped	100.00	51.80	100.00	0.00	100.00
# Depth per reference base for ALL data.
# Use 'grep ^FDP_ALL | cut -f 2-' to extract this part.
FDP_ALL	mixed_clipped	vir1	0,54	2,77	3,254	0,25	1,294	0,96
FDP_ALL	mixed_clipped	vir2	0,35	2,5	3,69	2,100	3,91	0,120	2,141	1,161	2,128	0,50
# Depth per reference base for full-length valid amplicon data.
# Use 'grep ^FDP_VALID | cut -f 2-' to extract this part.
FDP_VALID	mixed_clipped	vir1	0,54	2,331	0,415
FDP_VALID	mixed_clipped	vir2	0,35	1,5	2,260	0,120	1,430	0,50
# Distribution of aligned template coordinates.
# Use 'grep ^FTCOORD | cut -f 2-' to extract this part.
FTCOORD	mixed_clipped	1	55,385,2,0
FTCOORD	mixed_clipped	2
FTCOORD	mixed_clipped	3	36,300,2,0	41,300,1,0
FTCOORD	mixed_clipped	4
FTCOORD	mixed_clipped	5	421,850,2,0
# Classification of amplicon status.  Columns are
# number with both primers from this amplicon, number with
# primers from different amplicon, and number with a position
# not matching any valid amplicon primer site
# Use 'grep ^FAMP | cut -f 2-' to extract this part.
FAMP	mixed_clipped	0	8	0	2
FAMP	mixed_clipped	1	2	0	1
FAMP	mixed_clipped	2	0	0	1
FAMP	mixed_clipped	3	4	0	0
FAMP	mixed_clipped	4	0	0	0
FAMP	mixed_clipped	5	2	0	0
# Summary stats.
# Use 'grep ^CSS | cut -f 2-' to extract this part.
CSS	COMBINED	vir1	raw total sequences:	8
CSS	COMBINED	vir1	filtered sequences:	0
CSS	COMBINED	vir1	failed primer match:	2
CSS	COMBINED	vir1	matching sequences:	6
CSS	COMBINED	vir1	consensus depth count < 1 and >= 1:	649	0
CSS	COMBINED	vir2	raw total sequences:	10
CSS	COMBINED	vir2	filtered sequences:	0
CSS	COMBINED	vir2	failed primer match:	0
CSS	COMBINED	vir2	matching sequences:	10
CSS	COMBINED	vir2	consensus depth count < 1 and >= 1:	809	0
# Absolute matching read counts per amplicon.
# Use 'grep ^CREADS | cut -f 2-' to extract this part.
CREADS	COMBINED	5	1	6	0	4
CVDEPTH	COMBINED	2	0	2	0	1
CREADS	MEAN	5.0	1.0	6.0	0.0	4.0
CREADS	STDDEV	0.0	0.0	0.0	0.0	0.0
# Read percentage of distribution between amplicons.
# Use 'grep ^CRPERC | cut -f 2-' to extract this part.
CRPERC	COMBINED	31.250	6.250	37.500	0.000	25.000
CRPERC	MEAN	31.250	6.250	37.500	0.000	25.000
CRPERC	STDDEV	0.000	0.000	0.000	0.000	0.000
# Read depth per amplicon.
# Use 'grep ^CDEPTH | cut -f 2-' to extract this part.
CDEPTH	COMBINED	2.8	0.5	3.9	0.0	1.7
CDEPTH	MEAN	2.8	0.5	3.9	0.0	1.7
CDEPTH	STDDEV	0.0	0.0	0.0	0.0	0.0
CPCOV-1	MEAN	100.0	51.8	100.0	0.0	100.0
CPCOV-1	STDDEV	0.0	0.0	0.0	0.0	0.0
# Depth per reference base for ALL data.
# Use 'grep ^CDP_ALL | cut -f 2-' to extract this part.
CDP_ALL	COMBINED	vir1	0,54	2,77	3,254	0,25	1,294	0,96
CDP_ALL	COMBINED	vir2	0,35	2,5	3,69	2,100	3,91	0,120	2,141	1,161	2,128	0,50
# Depth per reference base for full-length valid amplicon data.
# Use 'grep ^CDP_VALID | cut -f 2-' to extract this part.
CDP_VALID	COMBINED	vir1	0,54	2,331	0,415
CDP_VALID	COMBINED	vir2	0,35	1,5	2,260	0,120	1,430	0,50
# Distribution of aligned template coordinates.
# Use 'grep ^CTCOORD | cut -f 2-' to extract this part.
CTCOORD	COMBINED	1	55,385,2,0
CTCOORD	COMBINED	2
CTCOORD	COMBINED	3	36,300,2,0	41,300,1,0
CTCOORD	COMBINED	4
CTCOORD	COMBINED	5	421,850,2,0
# Classification of amplicon status.  Columns are
# number with both primers from this amplicon, number with
# primers from different amplicon, and number with a position
# not matching any valid amplicon primer site
# Use 'grep ^CAMP | cut -f 2-' to extract this part.
CAMP	COMBINED	0	8	0	2
CAMP	COMBINED	1	2	0	1
CAMP	COMBINED	2	0	0	1
CAMP	COMBINED	3	4	0	0
CAMP	COMBINED	4	0	0	0
CAMP	COMBINED	5	2	0	0
