# 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 - 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