Á¦ÁÖ¹è²Å´ÞÆØÀÌ (Aegista (Aegista) chejuensis)



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¢Ã ±¹    ¸í: Á¦ÁÖ¹è²Å´ÞÆØÀÌ

¢Ã ÇР   ¸í: Aegista chejuensis Pilsbry & Hirase

¢Ã ÁöÁ¤¹øÈ£: °íÀ¯Á¾

¢Ã °è    Åë: º¹Á·°­-ÁøÀ¯Æó¸ñ-´ÞÆØÀ̰ú

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1) äÁýÁ¤º¸

- äÁýÇã°¡: °íÀ¯Á¾

- ä Áý ÀÚ: °­¿ø´ëÇб³ ÀÌÁØ»ó


2) äÁýÇöȲ ¹× »ùÇÃó¸®

Á¦ÁÖ¹è²Å´ÞÆØÀÌ Ã¤ÁýÇöȲ

»ùÇÃó¸®

äÁýÀÏ

°³Ã¼ ¼ö

DNAseq

RNAseq

Ç¥º»

2014.08.26

9 EA

4 EA

4 EA

1 EA


3) QC Data

»ùÇÃÁ¾

DNA QC

RNA QC

Result

Concentration (ug/ul)

Total Conc. (ug)

Concentration (ug/ul)

RIN (>7)

Á¦ÁÖ¹è²Å´ÞÆØÀÌ

113

9

254

9.8

pass


4) ±âÁ¸ NCBI Taxonomy À¯ÀüÁ¤º¸ ÇöȲ

À¯ÀüÁ¤º¸ Á¾·ù

Aegista ¼Ó À¯ÀüÀÚ¿ø

Aegista (Aegista) chejuensis

À¯ÀüÀÚ¿ø 

Nucleotide

359

-

Protein

251

-

Genome

2

-

Gene

74

-


5) Sequencing ºÐ¼® °á°ú

- Illumina DNA Sequncing °á°ú

Input information

¡¡

Region1

Region2

Region3

Region4

Total

raw data

Number Of Reads

118,506,288 

118,506,288 

10,275,102

10,275,102

257,562,780

Number Of Bases

14,931,792,288 

14,931,792,288 

1,294,662,852

1,294,662,852

32,452,910,280

error correction

Number Of Reads

109,658,743 

108,690,436 

4,491,029

4,422,673

227,262,881

Number Of Bases

12,563,157,322 

12,348,029,788

456,363,875

444,403,694

25,811,954,679

pair reads

Number Of Reads

 

209,527,066

 

6,725,334

216,252,400

Number Of Bases

 

24,031,628,914

 

713,837,970

24,745,466,884

single reads

Number Of Reads

 

8,822,113

 

2,188,368

11,010,481

Number Of Bases

 

879,558,196

 

186,929,599

1,066,487,795

Assembly Results

Scaffold Metrics

> 1 bp*

> 100 bp

> 500 bp**

> 1000 bp

> 2000 bp

Number Of Scaffolds

2,215,276

2,215,276

511,727

186,167

37,418

Number Of Bases

886,619,538

886,619,538

540,436,120

313,208,676

111,951,531

Avg. Scaffold Size

400

400

1,056

1,682

2,991

N50 Scaffold Size

680

680

1,137

1,659

2,791

N80 Scaffold Size

240

240

703

1,208

2,238

N90 Scaffold Size

148

148

595

1,097

2,111

largest Scaffold Size

99,405

99,405

99,405

99,405

99,405

Contig Metrics

> 1 bp*

> 100 bp

> 500 bp**

> 1000 bp

> 2000 bp

Number Of Contigs

21,540,436 

4,140,248 

258,618 

29,414 

2,596 

Number Of Bases

1,961,131,938 

968,202,411 

195,406,419 

45,440,146 

12,182,373 

Avg. Contig Size

91 

233 

755 

1,544 

4,692 

N50 Contig Size

96 

249 

717 

1,347 

5,704 

N80 Contig Size

50 

155 

568 

1,096 

2,685 

N90 Contig Size

47 

134 

532 

1,045 

2,240 

Largest Contig Size

70,769 

70,769 

70,769 

70,769 

70,769 

 

- Illumina RNA Sequncing °á°ú

Input information

¡¡

¡¡

¡¡

Region1

Region2

Total

raw data

Number Of Reads

 

 

128,327,935 

128,327,935 

256,655,870 

Number Of Bases

 

 

16,169,319,810 

16,169,319,810 

32,338,639,620 

error correction

Number Of Reads

 

 

127,109,211 

126,147,475 

253,256,686 

Number Of Bases

 

 

15,739,923,181 

15,660,526,491 

31,400,449,672 

pair reads

Number Of Reads

 

 

 

 

251,314,118 

Number Of Bases

 

 

 

 

31,188,107,081 

single reads

Number Of Reads

 

 

 

 

    1,942,568

Number Of Bases

 

 

 

 

212,342,591 

Assembly Results

Scaffold Metrics

> 1 bp*

> 100 bp

> 500 bp**

> 1000 bp

> 2000 bp

Number Of Scaffolds

    228,106

 228,106

  34,622

      11,146

     2,646  

Number Of Bases

74,648,423 

74,648,423 

35,620,275 

19,569,119 

8,016,049 

Avg. Scaffold Size

    327

     327

       1,028  

      1,755  

  3,029  

N50 Scaffold Size

    467

   467

   1,096  

 1,763  

   2,940  

N80 Scaffold Size

     189

    189

     667

   1,233  

2,278  

N90 Scaffold Size

      134

    134

     576

 1,108  

   2,128  

largest Scaffold Size

    14,943  

  14,943

      14,943

     14,943

   14,943

Contig Metrics

> 1 bp*

> 100 bp

> 500 bp**

> 1000 bp

> 2000 bp

Number Of Contigs

   3,795,144

321,887 

 22,581

     5,292  

    722

Number Of Bases

230,294,252 

74,003,080 

19,581,172 

7,973,399 

1,940,159 

Avg. Contig Size

      60

     229

   867

    1,506  

     2,687  

N50 Contig Size

    63

    261

     870

   1,472  

    2,638  

N80 Contig Size

      35

    138

    607

     1,148  

   2,164  

N90 Contig Size

    32

       115

      549

    1,066  

   2,077  

Largest Contig Size

 7,490

     7,490

      7,490  

       7,490  

    7,490  

³ª) ¸êÁ¾À§±âÁ¾ µ¿¹° Genome Survey

 

°Ë¼ö¿ë  »ùÇà DNA ³óµµ ¹× ÃÑ ¾ç, È®ÁõÇ¥º» ÇöȲǥ

¡¡Sample¸í

³óµµ(ng/ul)

Volume(ul)

DNA ÃÑ·®(ug)

O.D A260/280

È®ÁõÇ¥º»

äÁýÇã°¡ÀÏ

äÁýÀÏ

Á¦ÁÖ¹è²Å´ÞÆØÀÌ

152

996

151

1.54

¡Û

°íÀ¯Á¾

2014.8.26


(2) À¯Àüü ¼­¿­È®º¸ : ÇöÀç 20Á¾ È®º¸

Sample

±¸ºÐ

raw data size

trim data size

ºñ°í

Á¦ÁÖ¹è²Å´ÞÆØÀÌ

DNA

32,452,910,280

25,811,954,679

¡¡

RNA

32,338,639,620 

31,400,449,672 

¡¡


(3) ±âŸºÐ¼®

A. Genome Size estimation

»ù Çà ¸í

Kmer size

Kmer total

Pk depth

Genome_size

Coverage(X)

Á¦ÁÖ¹è²Å´ÞÆØÀÌ

23

18,486,980,928

178

103,859,443 

228.205

B. ¹Ýº¹¼­¿­

- ½ÃÄö½ÌÀÌ ¿Ï·áµÈ Á¦ÁÖ¹è²Å´ÞÆØÀÌ DNA ¹× RNAÀÇ contigs Áß 1kb ÀÌ»óÀÇ contigsÀÇ ¹Ýº¹¼­¿­À» Ž»ö(Left; Repeat masking results of DNA contigs, Right; Repeat masking results of RNA contigs).

sequences: 29,640

 

sequences: 5,292

total length: 45736033 bp (45736033 bp excl N/X-runs)

 

total length: 7,973,399 bp (7,973,399 bp excl N/X-runs)

GC level: 41.78%

 

GC level: 45.61%

bases masked: 60,083 bp (0.13%)

 

bases masked: 4079 bp (0.05%)

 

number of

elements

length

occupied

percentage

of sequence

 

 

number of

elements

length

occupied

percentage

of sequence

SINEs:          

8

367 bp

0.00%

 

SINEs:          

0

0 bp

0.00%

 

ALUs      

0

0 bp

0.00%

 

 

ALUs      

0

0 bp

0.00%

 

MIRs      

3

178 bp

0.00%

 

 

MIRs      

0

0 bp

0.00%

LINEs:          

106

24,847 bp

0.05%

 

LINEs:          

14

1,154 bp

0.01%

 

LINE1     

9

584 bp

0.00%

 

 

LINE1     

4

245 bp

0.00%

 

LINE2     

4

223 bp

0.00%

 

 

LINE2     

3

146 bp

0.00%

 

L3/CR1    

14

1,645 bp

0.00%

 

 

L3/CR1    

1

79 bp

0.00%

LTR elements:   

24

2,414 bp

0.01%

 

LTR elements:   

1

38 bp

0.00%

 

ERVL      

1

63 bp

0.00%

 

 

ERVL      

0

0 bp

0.00%

 

ERVL-MaLRs

0

0 bp

0.00%

 

 

ERVL-MaLRs

0

0 bp

0.00%

 

ERV_classI 

18

1,872 bp

0.00%

 

 

ERV_classI 

1

38 bp

0.00%

 

ERV_classII

0

0 bp

0.00%

 

 

ERV_classII

0

0 bp

0.00%

DNA elements:   

177

20,735 bp

0.05%

 

DNA elements:   

18

2,687 bp

0.03%

 

hAT-Charlie 

60

7,524 bp

0.02%

 

 

hAT-Charlie 

10

2,150 bp

0.03%

 

TcMar-Tigger

42

5,299 bp

0.01%

 

 

TcMar-Tigger

2

71 bp

0.00%

Unclassified:   

2

94 bp

0.00%

 

Unclassified:   

0

0 bp

0.00%

Total interspersed repeats:

 

48,457 bp

0.11%

 

Total interspersed repeats:

 

3,879 bp

0.05%

Small RNA:

99

11,300 bp

0.02%

 

Small RNA:

2

200 bp

0.00%

Satellites:

2

326 bp

0.00%

 

Satellites:

0

0 bp

0.00%

Simple repeats:

0

0 bp

0.00%

 

Simple repeats:

0

0 bp

0.00%

Low complexity:

0

0 bp

0.00%

 

Low complexity:

0

0 bp

0.00%



D. Mito-genome Map


±×¸²ÀÔ´Ï´Ù.
¿øº» ±×¸²ÀÇ À̸§: ½½¶óÀ̵å10.JPG
¿øº» ±×¸²ÀÇ Å©±â: °¡·Î 960pixel, ¼¼·Î 720pixel

(4) Microsatellite È帱º

A. SSR statistics

Motif(-mer)

2

3

4

5

6

7

8

9

10

Total

Á¦ÁÖ¹è²Å´ÞÆØÀÌ

5,633

2,311

626

17

14

5

7

1

3

8,617


B. ¹ÙÄڵ弭¿­

>Á¦ÁÖ¹è²Å´ÞÆØÀÌ(Aegista chejuensis)

ACTTTATATATATTATTTGGTGTTTGATGTGGAATAGTTGGATCTGGTTTATCATTATTA

ATCCGTATAGAATTAGGAACTTGTAATGTATTAAGCGATAGTCATTTTTTTAATGTTATT

GTTACAGCACATGCATTTGTAATAATCTTCTTTATAGTAATACCAATCATGATTGGTGGT

TTTGGAAACTGAATAGTTCCATTACTAATTGGGGCTCCTGATATAAGTTTTCCACGAATA

AATAATATAAGATTTTGATTATTACCACCTTCATTTATCTTATTAATTTCAAGAAGATTA

GTTGAAGGTGGGGCTGGAACTGGGTGAACTGTATATCCACCTTTAAGTTCAATTATAGGT

CATAGAGGTGCTTCAGTAGATTTAGCAATTTTTTCTTTACATTTAGCTGGAATATCATCT

ATTTTAGGTGCAATTAATTTTATTACTACAATTTTTAATATACGTAGGCCAGGAAACTCT

ATAGAACGATTAAGATTATTTGTATGATCTATTTTAATTACAGTATTTTTATTACTTCTA

TCATTACCTGTTTTAGCAGGTGCTATTACAATATTATTAACTGATCGAAATTTTAATACT

TCATTTTTTGATCCTGCAGGAGGAGGAGATCCTATTTTATATCAGCATTT


Lozekia deubeli : family ºÎÅÍ ´Ù¸§

Baudinella thielei :¡¡superfamily ºÎÅÍ ´Ù¸§


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