# Summary statistics, used for scaling the plots. SS Number of files: 4 SS Number of amplicons: 2 SS Reference length: 800 SS End of summary # Amplicon locations from BED file. # LEFT/RIGHT are - format and comma-separated for alt-primers. # # AMPLICON NUMBER LEFT RIGHT AMPLICON 1 31-54 386-410 AMPLICON 2 321-342 705-726 # Summary stats. # Use 'grep ^FSS | cut -f 2-' to extract this part. FSS 1_hard_clipped.expected raw total sequences: 8 FSS 1_hard_clipped.expected filtered sequences: 0 FSS 1_hard_clipped.expected failed primer match: 2 FSS 1_hard_clipped.expected matching sequences: 6 FSS 1_hard_clipped.expected consensus depth count < 1 and >= 1: 132 517 FSS 1_hard_clipped.expected consensus depth count < 20 and >= 20: 649 0 FSS 1_hard_clipped.expected consensus depth count < 100 and >= 100: 649 0 # Absolute matching read counts per amplicon. # Use 'grep ^FREADS | cut -f 2-' to extract this part. FREADS 1_hard_clipped.expected 5 1 FVDEPTH 1_hard_clipped.expected 2 0 # Read percentage of distribution between amplicons. # Use 'grep ^FRPERC | cut -f 2-' to extract this part. FRPERC 1_hard_clipped.expected 83.333 16.667 # Read depth per amplicon. # Use 'grep ^FDEPTH | cut -f 2-' to extract this part. FDEPTH 1_hard_clipped.expected 2.8 0.5 # Percentage coverage per amplicon # Use 'grep ^FPCOV | cut -f 2-' to extract this part. FPCOV-1 1_hard_clipped.expected 100.00 51.80 FPCOV-20 1_hard_clipped.expected 0.00 0.00 FPCOV-100 1_hard_clipped.expected 0.00 0.00 # Depth per reference base for ALL data. # Use 'grep ^FDP_ALL | cut -f 2-' to extract this part. FDP_ALL 1_hard_clipped.expected 0,54 2,77 3,254 0,25 1,294 0,96 # Depth per reference base for full-length valid amplicon data. # Use 'grep ^FDP_VALID | cut -f 2-' to extract this part. FDP_VALID 1_hard_clipped.expected 0,54 2,331 0,415 # Distribution of aligned template coordinates. # Use 'grep ^FTCOORD | cut -f 2-' to extract this part. FTCOORD 1_hard_clipped.expected 0 FTCOORD 1_hard_clipped.expected 1 FTCOORD 1_hard_clipped.expected 2 # 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 1_hard_clipped.expected 0 2 0 2 FAMP 1_hard_clipped.expected 1 2 0 1 FAMP 1_hard_clipped.expected 2 0 0 1 # Summary stats. # Use 'grep ^FSS | cut -f 2-' to extract this part. FSS 1_soft_clipped.expected raw total sequences: 8 FSS 1_soft_clipped.expected filtered sequences: 0 FSS 1_soft_clipped.expected failed primer match: 2 FSS 1_soft_clipped.expected matching sequences: 6 FSS 1_soft_clipped.expected consensus depth count < 1 and >= 1: 132 517 FSS 1_soft_clipped.expected consensus depth count < 20 and >= 20: 649 0 FSS 1_soft_clipped.expected consensus depth count < 100 and >= 100: 649 0 # Absolute matching read counts per amplicon. # Use 'grep ^FREADS | cut -f 2-' to extract this part. FREADS 1_soft_clipped.expected 5 1 FVDEPTH 1_soft_clipped.expected 2 0 # Read percentage of distribution between amplicons. # Use 'grep ^FRPERC | cut -f 2-' to extract this part. FRPERC 1_soft_clipped.expected 83.333 16.667 # Read depth per amplicon. # Use 'grep ^FDEPTH | cut -f 2-' to extract this part. FDEPTH 1_soft_clipped.expected 2.8 0.5 # Percentage coverage per amplicon # Use 'grep ^FPCOV | cut -f 2-' to extract this part. FPCOV-1 1_soft_clipped.expected 100.00 51.80 FPCOV-20 1_soft_clipped.expected 0.00 0.00 FPCOV-100 1_soft_clipped.expected 0.00 0.00 # Depth per reference base for ALL data. # Use 'grep ^FDP_ALL | cut -f 2-' to extract this part. FDP_ALL 1_soft_clipped.expected 0,54 2,77 3,254 0,25 1,294 0,96 # Depth per reference base for full-length valid amplicon data. # Use 'grep ^FDP_VALID | cut -f 2-' to extract this part. FDP_VALID 1_soft_clipped.expected 0,54 2,331 0,415 # Distribution of aligned template coordinates. # Use 'grep ^FTCOORD | cut -f 2-' to extract this part. FTCOORD 1_soft_clipped.expected 0 FTCOORD 1_soft_clipped.expected 1 FTCOORD 1_soft_clipped.expected 2 # 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 1_soft_clipped.expected 0 2 0 2 FAMP 1_soft_clipped.expected 1 2 0 1 FAMP 1_soft_clipped.expected 2 0 0 1 # Summary stats. # Use 'grep ^FSS | cut -f 2-' to extract this part. FSS 1_soft_clipped_strand.expected raw total sequences: 8 FSS 1_soft_clipped_strand.expected filtered sequences: 0 FSS 1_soft_clipped_strand.expected failed primer match: 2 FSS 1_soft_clipped_strand.expected matching sequences: 6 FSS 1_soft_clipped_strand.expected consensus depth count < 1 and >= 1: 132 517 FSS 1_soft_clipped_strand.expected consensus depth count < 20 and >= 20: 649 0 FSS 1_soft_clipped_strand.expected consensus depth count < 100 and >= 100: 649 0 # Absolute matching read counts per amplicon. # Use 'grep ^FREADS | cut -f 2-' to extract this part. FREADS 1_soft_clipped_strand.expected 5 1 FVDEPTH 1_soft_clipped_strand.expected 2 0 # Read percentage of distribution between amplicons. # Use 'grep ^FRPERC | cut -f 2-' to extract this part. FRPERC 1_soft_clipped_strand.expected 83.333 16.667 # Read depth per amplicon. # Use 'grep ^FDEPTH | cut -f 2-' to extract this part. FDEPTH 1_soft_clipped_strand.expected 2.8 0.5 # Percentage coverage per amplicon # Use 'grep ^FPCOV | cut -f 2-' to extract this part. FPCOV-1 1_soft_clipped_strand.expected 100.00 51.80 FPCOV-20 1_soft_clipped_strand.expected 0.00 0.00 FPCOV-100 1_soft_clipped_strand.expected 0.00 0.00 # Depth per reference base for ALL data. # Use 'grep ^FDP_ALL | cut -f 2-' to extract this part. FDP_ALL 1_soft_clipped_strand.expected 0,54 2,77 3,254 0,21 1,298 0,96 # Depth per reference base for full-length valid amplicon data. # Use 'grep ^FDP_VALID | cut -f 2-' to extract this part. FDP_VALID 1_soft_clipped_strand.expected 0,54 2,331 0,415 # Distribution of aligned template coordinates. # Use 'grep ^FTCOORD | cut -f 2-' to extract this part. FTCOORD 1_soft_clipped_strand.expected 0 FTCOORD 1_soft_clipped_strand.expected 1 FTCOORD 1_soft_clipped_strand.expected 2 # 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 1_soft_clipped_strand.expected 0 2 0 2 FAMP 1_soft_clipped_strand.expected 1 2 0 1 FAMP 1_soft_clipped_strand.expected 2 0 0 1 # Summary stats. # Use 'grep ^FSS | cut -f 2-' to extract this part. FSS 2_both_clipped.expected raw total sequences: 2 FSS 2_both_clipped.expected filtered sequences: 0 FSS 2_both_clipped.expected failed primer match: 0 FSS 2_both_clipped.expected matching sequences: 2 FSS 2_both_clipped.expected consensus depth count < 1 and >= 1: 319 330 FSS 2_both_clipped.expected consensus depth count < 20 and >= 20: 649 0 FSS 2_both_clipped.expected consensus depth count < 100 and >= 100: 649 0 # Absolute matching read counts per amplicon. # Use 'grep ^FREADS | cut -f 2-' to extract this part. FREADS 2_both_clipped.expected 2 0 FVDEPTH 2_both_clipped.expected 2 0 # Read percentage of distribution between amplicons. # Use 'grep ^FRPERC | cut -f 2-' to extract this part. FRPERC 2_both_clipped.expected 100.000 0.000 # Read depth per amplicon. # Use 'grep ^FDEPTH | cut -f 2-' to extract this part. FDEPTH 2_both_clipped.expected 2.0 0.0 # Percentage coverage per amplicon # Use 'grep ^FPCOV | cut -f 2-' to extract this part. FPCOV-1 2_both_clipped.expected 100.00 0.00 FPCOV-20 2_both_clipped.expected 0.00 0.00 FPCOV-100 2_both_clipped.expected 0.00 0.00 # Depth per reference base for ALL data. # Use 'grep ^FDP_ALL | cut -f 2-' to extract this part. FDP_ALL 2_both_clipped.expected 0,54 2,331 0,415 # Depth per reference base for full-length valid amplicon data. # Use 'grep ^FDP_VALID | cut -f 2-' to extract this part. FDP_VALID 2_both_clipped.expected 0,54 2,331 0,415 # Distribution of aligned template coordinates. # Use 'grep ^FTCOORD | cut -f 2-' to extract this part. FTCOORD 2_both_clipped.expected 0 FTCOORD 2_both_clipped.expected 1 FTCOORD 2_both_clipped.expected 2 # 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 2_both_clipped.expected 0 2 0 0 FAMP 2_both_clipped.expected 1 2 0 0 FAMP 2_both_clipped.expected 2 0 0 0 # Summary stats. # Use 'grep ^CSS | cut -f 2-' to extract this part. CSS COMBINED raw total sequences: 26 CSS COMBINED filtered sequences: 0 CSS COMBINED failed primer match: 6 CSS COMBINED matching sequences: 20 CSS COMBINED consensus depth count < 1 and >= 1: 649 0 CSS COMBINED consensus depth count < 20 and >= 20: 649 0 CSS COMBINED consensus depth count < 100 and >= 100: 649 0 # Absolute matching read counts per amplicon. # Use 'grep ^CREADS | cut -f 2-' to extract this part. CREADS COMBINED 17 3 CVDEPTH COMBINED 8 0 CREADS MEAN 4.2 0.8 CREADS STDDEV 1.3 0.4 # Read percentage of distribution between amplicons. # Use 'grep ^CRPERC | cut -f 2-' to extract this part. CRPERC COMBINED 87.500 12.500 CRPERC MEAN 87.500 12.500 CRPERC STDDEV 7.217 7.217 # Read depth per amplicon. # Use 'grep ^CDEPTH | cut -f 2-' to extract this part. CDEPTH COMBINED 10.4 1.6 CDEPTH MEAN 2.6 0.4 CDEPTH STDDEV 0.3 0.2 CPCOV-1 MEAN 100.0 38.9 CPCOV-1 STDDEV 0.0 22.4 CPCOV-20 MEAN 0.0 0.0 CPCOV-20 STDDEV 0.0 0.0 CPCOV-100 MEAN 0.0 0.0 CPCOV-100 STDDEV 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 0,54 8,77 11,254 0,21 1,4 3,294 0,96 # Depth per reference base for full-length valid amplicon data. # Use 'grep ^CDP_VALID | cut -f 2-' to extract this part. CDP_VALID COMBINED 0,54 8,331 0,415 # Distribution of aligned template coordinates. # Use 'grep ^CTCOORD | cut -f 2-' to extract this part. CTCOORD COMBINED 0 CTCOORD COMBINED 1 CTCOORD COMBINED 2 # 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 6 CAMP COMBINED 1 8 0 3 CAMP COMBINED 2 0 0 3