NFINtb Nothobranchius furzeri transcriptome browser

Libraries

LibraryNameClonesRaw ESTsHigh quality ESTsMean EST lengthstd EST length
1GRZ_Bank1_Sanger131808131808129826698.6136.9
2GRZ_Bank1_454751885751885662494212.242.6
3GRZ_Bank2_454415426415426342570218.340.7
4GRZ_Bank3_454235123623512362136328367.6101.2
5GRZ_Bank5_Illumina897309108973091089730910151.00.0
6GRZ_Bank6_Illumina554100425541004255410042101.00.0
6GRZ_Bank6_Illumina33947044339470443394704476.00.0
7GRZ_Bank7_Illumina609978206099782060997820101.00.0
7GRZ_Bank7_Illumina36117265361172653611726576.00.0
8GRZ_Bank8_Illumina35963921359639213596392176.00.0
9GRZ_Bank9_Illumina27369310273693102736931076.00.0
10GRZ_Bank10_Illumina31727935317279353172793576.00.0
11GRZ_Bank11_Illumina34720289347202893472028976.00.0
12GRZ_Bank12_Illumina30268649302686493026864976.00.0
13GRZ_Bank13_Illumina31423327314233273142332776.00.0

 


cDNA contigs

Minimum length (bp): 300
Maximum length (bp): 64116
Average length (bp): 1183.8

from (bp)to (bp)number of contigs
30059996735
60099937928
1000199948605
2000299914331
300039997918
400049993600
500099994274
1000014999211
150001999915
20000650004

 


Annotation

Annotation statistics

Number of annotated cDNA contigs: 112853 (52.8%)
Number of full length cDNA contigs: 32813 (15.4%)

cDNA contig with blast hits

DatabaseNumber of contigs%
any_database12602359.0
ensembl_fish_cdna10012346.9
ensembl_fish_proteins10130947.4
genage_human142866.7
ncbi_fish_unigenes11026751.6
nr10036947.0
refseq_human_proteins8271938.7
uniprot10180447.7
Any database12602359.0

cDNA contigs with predicted structural domains

DatabaseNumber of contigs%
any_database3846118.0
pfam3846118.0
Any database3846118.0

cDNA contigs with orthologues

DatabaseNumber of contigs%
any_database00.0

 


SSRs and Contamination

SNP and SNV statistics

SNP transversions: 47651 (38.5%)
SNP transitions: 76123 (61.5%)

SNV transversions: 44270 (38.4%)
SNV transitions: 70948 (61.6%)

 

MutationNumber of SNP
A<->C6437
A<->G18840
A<->T7255
C<->A6124
C<->G4463
C<->T19607
G<->A19152
G<->C4224
G<->T6307
T<->A6883
T<->C18524
T<->G5958

 

MutationNumber of SNV
A<->C5673
A<->G17132
A<->T6921
C<->A6210
C<->G3851
C<->T19194
G<->A18512
G<->C3556
G<->T6342
T<->A6460
T<->C16110
T<->G5257

Number of transcripts with indels: 0 (0.0%)

 

Microsatellites detected by sputnik

LocationNumber of microsatellites
3 utr10725
in orf9646
5 utr6193
other1315
Total27879
 
UnitNumber of microsatellites
AC12371
A2258
AGG1476
AAT1357
AG1246
ATC871
AT750
AAAT733
AAG642
ATCC563
AGC542
C429
AAC368
AAAC347
AGAT282
AAAG262
AATC253
ACC227
ACGC221
AATTC218
AAAAT210
AATG199
ACTC185
ACT158
AATAG142
ACAT129
ACAG127
AAAAC99
ACCAT83
AAAAG69
AATGG68
AGGG67
AACT54
AAGG48
ACG43
AAGT42
AAATC37
AACC30
AGAGG29
AATCC27
CCG24
AACAC22
AAGAT22
AGCGG22
AAATT20
AACTG19
ACGAG19
ACCGG18
AATAT17
AATCT17
AGGC17
AAACT16
ACACT16
AACAT15
AAGCT15
ACTCT15
ACTG15
AAACC14
ACCCC14
ACCT13
AATT12
ACACC12
ACTCC12
AGCT12
ACCCG10
AGCCT10
ACAGG9
ACGAT9
ACGT9
AAATG8
CG8
AACAG7
AACCC7
ACCAG7
AGATC7
AGGGC7
AATGT6
ACGG6
AGATG6
AGCG6
AGCTC6
ATGCC6
AAAGT5
AAGAG5
ACCTC5
ACGCC5
ACTAG5
AGCAT5
AACCT4
AACG4
AACGT4
AACTT4
AAGGC4
AAGTG4
AATAC4
ACATC4
ACCCT4
ACCTG4
ACTAT4
AGGCG4
CCCCG4
AACCG3
AACGC3
AAGAC3
AAGGG3
ACCC3
AGAGC3
AGCC3
AGCCG3
CCCGG3
AAGTC2
ACAGC2
ACAGT2
ACCGT2
ACGCT2
ACGGG2
AGCCC2
AGGGG2
AAAGG1
AACTC1
ACATG1
AGCGC1
AGGAT1
AGGCC1
ATATC1
Total27926

 

Contamination statistics

OriginNumber of contigs
fungi154
invertebrate1495
microbial21
plant581
protozoa926
vertebrate_mammalian4208
Total7385
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