stats.md

Statistics

Extension

File Extension	Count
gff	13
gff3	153

Headers

Header Key	Value	Percentage Using at least Once
#	59	17.47%
FASTA	2	1.20%
Index-subfeatures	2	1.20%
NOTE:	1	0.60%
Type	1	0.60%
attribute-ontology	1	0.60%
color-code	1	0.60%
date	2	1.20%
feature-ontology	6	3.61%
genome-build	2	1.20%
gff-version 3	3	1.81%
gff-version 3	1	0.60%
gff-version 2	1	0.60%
gff-version 3	164	83.13%
hdr	1	0.60%
history	3	0.60%
line-order	1	0.60%
max-num-mismatches	1	0.60%
max-read-length	1	0.60%
primer-base	1	0.60%
sequence-region	274	56.63%
solid-gff-version	1	0.60%
source	1	0.60%
source-ontology	1	0.60%
source-version	1	0.60%
species	8	4.82%
time	1	0.60%

Tabs

Tabs In Line	Count
10	140
9	1286559

Tools

Tools	Count
feature	31
GenBank	22
.	19
CPT_ShineFind	8
CPT	8
annotation	7
RefSeq	6
maker	6
getOrfsOrCds	6
blast	6
blastn	6
est2genome	6
FlyBase	5
progressiveMauve	5
AU9	5
glimmer	4
TMHMM	4
DGRC_1	3
example	3
cpt.fixModel	3

Feature Types

Feature	Count
match_part	644648
match	314926
orthologous_to	57863
Z_over_Input	50198
CDS	42052
exon	18843
TF_binding_site	15781
mRNA	15676
gene	11570
RNAi_reagent	9416
oligonucleotide	9257
paralogous_to	8610
oligo	8303
protein_coding_gene	7969
polypeptide_region	6555
Shine_Dalgarno_sequence	5813
Match	5635
transposable_element_insertion_site	4837
five_prime_UTR	4785
intron	4774
exon_junction	4709
three_prime_UTR	3722
polyA_site	3425
contig	2204
TSS	1990
golden_path	1817
region	1753
BAC_cloned_genomic_insert	1603
regulatory_region	1491
stop_codon	1425
start_codon	1423
orthologous_region	1382
protein	1105
polypeptide	1062
sgRNA	940
Topological domain	898
origin_of_replication	568
insulator	556
deletion	556
pcr_product	556
PCR_product	500
Transmembrane	454
Chain	453
point_mutation	396
chromosome_breakpoint	350
repeat_region	313
chromosome_band	304
terminator	260
breakpoint	234
ncRNA	233
delins	181
tRNA	132
protein_binding_site	126
protein_match	126
ncRNA_gene	115
read	112
sequence_feature	106
transposable_element	102
sequence_variant	91
HSP	88
insertion_site	83
pseudogene	72
tandem_repeat	58
pseudogenic_transcript	54
modified_RNA_base_feature	53
Beta strand	47
non_canonical_five_prime_splice_site	47
transcript	45
rescue_region	44
syntenic_region	44
non_canonical_three_prime_splice_site	41
mature_protein_region	38
rescue_fragment	34
experimental_result_region	34
long_terminal_repeat	32
remark	31
binding_site	29
ARS	26
noncoding_exon	26
insertion	25
expressed_sequence_match	24
Disulfide bond	22
miRNA	20
silencer	20
Lipobox	20
cds	18
nucleotide_to_protein_match	16
polypeptide_domain	15
pre_miRNA	14
MNV	11
rRNA	11
Helix	10
enhancer	10
my_feature	10
motif	10
Glycosylation	9
snoRNA	9
DNA	9
Peptide	8
misc_feature	8
SNP	8
transposable_element_gene	8
complex_substitution	7
snRNA	7
supercontig	7
regulatory	7
micro_array_oligo	7
nucleotide_match	7
Domain	6
Nucleotide binding	6
promoter	6
recombination_feature	6
loop	6
EST_match	6
Site	5
Turn	5
chromosome	5
Active site	4
stop_codon_read_through	4
peptide_helix	4
telomere	4
LTR_retrotransposon	4
sequence_alteration	3
mature_peptide	3
mobile_genetic_element	3
5'-UTR	3
gene_component_region	3
STS	3
sequence_difference	3
direct_repeat	3
Signal peptide	2
Propeptide	2
Non-terminal residue	2
BAC	2
coding	2
processed_transcript	2
3'-UTR	2
biological_region	2
protein_coding_primary_transcript	2
UTR	2
centromere	2
Region	1
DNA binding	1
Modified residue	1
chromosome_arm	1
right_end_read	1
left_end_read	1
trace	1
ultracontig	1
lincRNA_gene	1
lincRNA	1
signal_peptide	1
inverted_repeat	1
scaffold	1
clone_start	1
clone_end	1

Feature (Using SO term)	Count

Scores?

Score Range	Count
Does Not Use Scores	113
[0, 100]	30
[0, 10000]	13
[-2.8, 8728.0]	2
[102.0, 17680.0]	2
[-33.075, 76535.0]	1
[-4438.107454, -183.539619]	1
[-11.2071, 9.9974]	1
[-37.0, 336.0]	1
[-37.0, 207.0]	1
[0, 1000]	1

Tags

Tag	Value	Percentage Using at least Once
Name	1070347	322393.67%
Target	832972	250895.18%
target_type	808204	243434.94%
Parent	742440	223626.51%
ID	568467	171225.00%
program	307207	92532.23%
programversion	307207	92532.23%
sourcename	307207	92532.23%
Dbxref	127851	38509.34%
qseq	69585	20959.34%
sseq	69585	20959.34%
to_species	67899	20451.51%
to_name	66473	20021.99%
diopt_source	60884	18338.55%
__.__	50273	15142.47%
Alias	39408	11869.88%
library	35910	10816.27%
description	18771	5653.92%
bound_moiety	17925	5399.10%
gene_id	16458	4957.23%

Percent Encoding

Tag	Value	Count
%2C	,	20561
%20		13404
%3D	=	9337
%2A	*	5069
%3B	;	2164
%2B	+	1415
%7C	`	`
%28	(	979
%29	)	979
%40	@	856
%27	'	596
%25	%	154
%26	&	145
%23	#	118
%C3	�	115
%C2	�	106
%2F	/	74
%C4	�	26
%87	�	8
%80	�	6

Non-percent encoded values

Tag	Count
0x20	2710255
0xa	1286558

Trailing Semicolon in field 9

Tag	Count
random-gff3s-from-helena/yeast_chr1+2.gff3	616
random-gff3s-from-helena/Genus_species.gff3	116
random-gff3s-from-helena/annot_mapped.gff3	38
gffutils/glimmer_nokeyval.gff3	4
gffutils/gms2_example.gff3	4
gffutils/FBgn0031208.gff	3
gffutils/unsanitized.gff	1

Top Level Features

Tag	Count
match	313671
orthologous_to	57863
Z_over_Input	50198
TF_binding_site	15781
gene	11570
RNAi_reagent	9416
oligonucleotide	9257
paralogous_to	8610
oligo	8303
protein_coding_gene	7969
polypeptide_region	6555
Match	5635
CDS	5408
transposable_element_insertion_site	4837
exon_junction	4709
polyA_site	3414
TSS	1990
golden_path	1817
region	1743
BAC_cloned_genomic_insert	1603
regulatory_region	1491
orthologous_region	1382
protein	1104
polypeptide	1062
sgRNA	940
Shine_Dalgarno_sequence	860
origin_of_replication	568
insulator	556
deletion	556
pcr_product	556
PCR_product	500
Chain	453
point_mutation	396
chromosome_breakpoint	350
repeat_region	312
chromosome_band	304
terminator	260
breakpoint	229
delins	181
protein_binding_site	126
protein_match	126
ncRNA_gene	115
read	112
sequence_feature	106
transposable_element	102
insertion_site	83
mRNA	82
tandem_repeat	58
pseudogene	58
modified_RNA_base_feature	53
Beta strand	47
rescue_region	44
syntenic_region	44
transcript	42
mature_protein_region	36
rescue_fragment	34
experimental_result_region	34
long_terminal_repeat	32
remark	31
sequence_variant	30
ARS	26
insertion	25
expressed_sequence_match	24
Disulfide bond	22
miRNA	20
silencer	20
binding_site	19
contig	18
tRNA	18
nucleotide_to_protein_match	16
polypeptide_domain	15
MNV	11
Helix	10
enhancer	10
my_feature	10
motif	10
Glycosylation	9
DNA	9
Peptide	8
misc_feature	8
SNP	8
transposable_element_gene	8
complex_substitution	7
micro_array_oligo	7
Domain	6
Nucleotide binding	6
promoter	6
regulatory	6
loop	6
EST_match	6
Site	5
Turn	5
chromosome	5
Active site	4
peptide_helix	4
telomere	4
LTR_retrotransposon	4
sequence_alteration	3
mobile_genetic_element	3
recombination_feature	3
sequence_difference	3
direct_repeat	3
snoRNA	3
Signal peptide	2
Propeptide	2
Non-terminal residue	2
BAC	2
coding	2
processed_transcript	2
biological_region	2
protein_coding_primary_transcript	2
ncRNA	2
centromere	2
Region	1
DNA binding	1
Modified residue	1
chromosome_arm	1
trace	1
ultracontig	1
lincRNA_gene	1
STS	1
inverted_repeat	1
scaffold	1
supercontig	1
snRNA	1