| Column | Description |
|---|---|
| RANKNAME | (REPLICON) = replicon name (source + plasmid/chr) (STRAIN) = strain name (SPECIES) = species name (GENUS) = genus name ... |
| NUM_SUBRANKS | = no. of distinct subranks for the current rank (E.g. the no. of SPECIES under the current GENUS) |
| GPROJ_ENTRIES | = no. of genome projects (i.e. STRAINS) under this RANK NAME |
| LINEAR_LENGTH | = N/O_LENGTH = non-overlapping length = no. of non-overlapping bases covering the unique DB |
| UNIQUE_DB_LENGTH | = no. of unique bases for this organism |
| FULL_REFDB_LENGTH | = no. of bases in full reference |
| LINEAR_COV | = LINEAR_LENGTH / UNIQUE_DB_LENGTH |
| HIT_COUNT | = no. of hits recruited to genome |
| HIT_COUNT_PLASMID | = no. of hits recruited to plasmid |
| READ_COUNT | = no. of reads recruited to genome |
| FULL_HIT_COUNT | = no. of full-length read hits recruited to genome |
| TOTAL_BP_MAPPED | = sum total of all hit lengths recruited to genome = hit1.length + hit2.length + ... hitX.length [formerly FOLD_COV_UNIQUE_SAMPLE] |
| LINEAR_DOC | = linear depth-of-coverage = fold coverage of sample's LINEAR_LENGTH = TOTAL_BP_MAPPED / LINEAR_LENGTH [formerly FOLD_COV_UNIQUE_REFDB] |
| UREF_DOC | = unique reference's depth-of-coverage = fold coverage of reference's UNIQUE_DB_LENGTH = TOTAL_BP_MAPPED / UNIQUE_DB_LENGTH |
| UREF_CMAX | = MAX COVERAGE OF REFDB POSSIBLE, GIVEN SAMPLE INPUT BASES = Cmax = L0/l0 = TOTAL_INPUT_BASES / UNIQUE_DB_LENGTH |
| FRAC_HITS_POSSIBLE | = HIT_COUNT / TOTAL_INPUT_READS |
| FRAC_BASES_POSSIBLE | = TOTAL_BP_MAPPED / TOTAL_INPUT_BASES |
| MEAN_HIT_LENGTH | = TOTAL_BP_MAPPED / HIT_COUNT |
| MEAN_LINEAR_HIT_LENGTH | = LINEAR_LENGTH / HIT_COUNT |
| best_SUBRANK | = name of the best subrank (determined by the highest LINEAR_COV) |
| best_NUM_SUBRANKS | = no. of subranks supporting current "SUBRANK" {SS} = no. of GI entries supporting this strain {S} = no. of strains supporting this species {G} = no. of species supporting this genus {F} = no. of genera supporting this family {O} = no. of families supporting this order {C} = no. of orders supporting this class {P} = no. of classes supporting this phylum |
| best_GPROJ_ENTRIES | = no. of genome projects (i.e. STRAINS) under this best_SUBRANK {SS} = no. of genome projects supporting this strain = 1 {S} = no. of genome projects supporting this species {G} = no. of genome projects supporting this genus {F} = no. of genome projects supporting this family {O} = no. of genome projects supporting this order {C} = no. of genome projects supporting this class {P} = no. of genome projects supporting this phylum |
| best_LINEAR_LENGTH | |
| best_UNIQUE_DB_LENGTH | |
| best_FULL_REFDB_LENGTH | |
| best_LINEAR_COV | |
| best_HIT_COUNT | |
| best_FULL_HIT_COUNT | |
| best_TOTAL_BP_MAPPED | |
| best_LINEAR_DOC (a.k.a. Abundance) | |
| best_UREF_DOC | |
| best_UREF_CMAX | |
| best_FRAC_HITS_POSSIBLE | |
| best_FRAC_BASES_POSSIBLE | |
| best_MEAN_HIT_LENGTH | |
| best_MEAN_LINEAR_HIT_LENGTH | |
| CONTIG_COUNT | = No. of contiguous fragments (after mapping & generating non-overlapping fragments) |
| CONTIG_MEAN_LEN | = Mean length of contigs (bp) |
| CONTIG_STDEV_LEN | = Standard deviation of contig lengths (bp) |
| CONTIG_MINLEN | = Length of smallest contig |
| CONTIG_MAXLEN | = Length of largest contig |
| CONTIG_HISTOGRAM(LEN:FREQ) | = Contig Length Histogram (in the format contigLength:frequency) |