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Vt (view source)

Revision as of 17:00, 5 October 2015

6,441 bytes added ,  17:00, 5 October 2015
→‎Annotate Indels
Line 1,201: Line 1,201:  
   20      100699  .      C      T      809.09  .      NSAMPLES=1;E=28;N=61;ESUM=28;NSUM=61;FLANKSEQ=GGTGAAAAAT[C/T]ACCTGTCAGT
 
   20      100699  .      C      T      809.09  .      NSAMPLES=1;E=28;N=61;ESUM=28;NSUM=61;FLANKSEQ=GGTGAAAAAT[C/T]ACCTGTCAGT
 
   20      101362  .      G      A      1087.13 .      NSAMPLES=1;E=36;N=67;ESUM=36;NSUM=67;FLANKSEQ=TAATACTGAA[G/A]TTTACTTCTC
 
   20      101362  .      G      A      1087.13 .      NSAMPLES=1;E=36;N=67;ESUM=36;NSUM=67;FLANKSEQ=TAATACTGAA[G/A]TTTACTTCTC
 +
 +
  The following shows the trace of how the algorithm works
 +
 +
    ============================================
 +
    ANNOTATING INDEL FUZZILY
 +
    ********************************************
 +
    EXTRACTIING REGION BY EXACT LEFT AND RIGHT ALIGNMENT
 +
   
 +
    20:131948:C/CCA
 +
    EXACT REGION 131948-131965 (18)
 +
                CCACACACACACACACAA
 +
    FINAL EXACT REGION 131948-131965 (18)
 +
                      CCACACACACACACACAA
 +
    ********************************************
 +
    PICK CANDIDATE MOTIFS
 +
   
 +
    Longest Allele : C[CA]CACACACACACACACAA
 +
    detecting motifs for an str
 +
    seq: CCACACACACACACACACAA
 +
    len : 20
 +
    cmax_len : 10
 +
    candidate motifs: 25
 +
    AC : 0.894737 2 0
 +
    AAC : 0.5 3 0.0555556
 +
    ACC : 0.5 3 0.0555556
 +
    AAAC : 0.0588235 4 0.125 (< 2 copies)
 +
    ACCC : 0.0588235 4 0.125 (< 2 copies)
 +
    AACAC : 0.5 5 0.02
 +
    ACACC : 0.5 5 0.02
 +
    AAACAC : 0.0666667 6 0.0555556 (< 2 copies)
 +
    ACACCC : 0.0666667 6 0.0555556 (< 2 copies)
 +
    AACACAC : 0.5 7 0.0102041
 +
    ACACACC : 0.5 7 0.0102041
 +
    AAACACAC : 0.0769231 8 0.03125 (< 2 copies)
 +
    ACACACCC : 0.0769231 8 0.03125 (< 2 copies)
 +
    AACACACAC : 0.5 9 0.00617284 (< 2 copies)
 +
    ACACACACC : 0.5 9 0.00617284 (< 2 copies)
 +
    AAACACACAC : 0.0909091 10 0.02 (< 2 copies)
 +
    ACACACACCC : 0.0909091 10 0.02 (< 2 copies)
 +
    ********************************************
 +
    PICKING NEXT BEST MOTIF
 +
   
 +
    selected:        AC 0.89 0.00
 +
    selected:        AC 0.89 0.00
 +
    ********************************************
 +
    4. DETECTING REPEAT TRACT FUZZILY
 +
    ++++++++++++++++++++++++++++++++++++++++++++
 +
    4a. Exact left/right alignment
 +
   
 +
    repeat_tract              : CACACACACACACACA
 +
    position                  : [131949,131964]
 +
    motif_concordance        : 1
 +
    repeat units              : 8
 +
    exact repeat units        : 8
 +
    total no. of repeat units : 8
 +
   
 +
    ++++++++++++++++++++++++++++++++++++++++++++
 +
    4a. Fuzzy right alignment
 +
    17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)[[User:Atks|Atks]] ([[User talk:Atks|talk]]) 17:00, 5 October 2015 (EDT)
 +
   
 +
    repeat motif : CA
 +
    rflank      : AACTC
 +
    mlen        : 2
 +
    rflen        : 5
 +
    plen        : 111
 +
   
 +
    read        : AGAAATGATAGTCACTTCAACAGATGGTGTTGGGAAAACTGGATTTCCACAGGCAGAACAAATGAAATGGATCCTTATCTTACACCACACACACACACACAAACTC
 +
    rlen        : 106
 +
   
 +
    optimal score: 50.5073
 +
    optimal state: MR
 +
    optimal track: MR|r|0|5
 +
    optimal probe len: 25
 +
    optimal path length : 107
 +
    max j: 106
 +
    probe: (1~82) [1~10] (1~5)
 +
    read : (1~82) [83~101] (102~106)
 +
   
 +
    motif #          : 10 [83,101]
 +
    motif concordance : 0.95% (9/10)
 +
    motif discordance : 0|1|0|0|0|0|0|0|0|0
 +
   
 +
    Model:  ----------------------------------------------------------------------------------CACACACACACACACACACAAACTC
 +
          SYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYMMMDMMMMMMMMMMMMMMMMMMMMME
 +
                                                                                              oo++oo++oo++oo++oo++RRRRR
 +
    Read:  AGAAATGATAGTCACTTCAACAGATGGTGTTGGGAAAACTGGATTTCCACAGGCAGAACAAATGAAATGGATCCTTATCTTACAC-CACACACACACACACAAACTC
 +
    17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)[[User:Atks|Atks]] ([[User talk:Atks|talk]]) 17:00, 5 October 2015 (EDT)
 +
   
 +
    ++++++++++++++++++++++++++++++++++++++++++++
 +
    4b. Fuzzy left alignment
 +
    17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)[[User:Atks|Atks]] ([[User talk:Atks|talk]]) 17:00, 5 October 2015 (EDT)
 +
   
 +
    QUAL+33 MATCH MISMATCH PENALTY
 +
    42 2.10001 -5.10001 -2.10001
 +
   
 +
    lflank      : ATCTTA
 +
    repeat motif : CA
 +
    lflen        : 6
 +
    mlen        : 2
 +
    plen        : 111
 +
   
 +
    read        : ATCTTACACCACACACACACACACAAACTCAAAATGGATTTAAAGACTTAAATGTGAGCCTGGCAAACTTAAAACTCCTAAAATAAAACAGAAGGGAATATCTTT
 +
    rlen        : 105
 +
   
 +
    optimal score: 50.5858
 +
    optimal state: Z
 +
    optimal track: Z|m|10|2
 +
    optimal probe len: 26
 +
    optimal path length : 106
 +
    max j: 105
 +
    mismatch penalty: 3
 +
   
 +
    model: (1~6) [1~10]
 +
    read : (1~6) [7~25][26~106]
 +
   
 +
    motif #          : 10 [7,25]
 +
    motif concordance : 0.95% (9/10)
 +
    motif discordance : 0|1|0|0|0|0|0|0|0|0
 +
   
 +
    Model:  ATCTTACACACACACACACACACACA--------------------------------------------------------------------------------
 +
          SMMMMMMMMMDMMMMMMMMMMMMMMMMZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZE
 +
            LLLLLLoo++oo++oo++oo++oo++                                                                               
 +
    Read:  ATCTTACAC-CACACACACACACACAAACTCAAAATGGATTTAAAGACTTAAATGTGAGCCTGGCAAACTTAAAACTCCTAAAATAAAACAGAAGGGAATATCTTT
 +
    17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)17:00, 5 October 2015 (EDT)[[User:Atks|Atks]] ([[User talk:Atks|talk]]) 17:00, 5 October 2015 (EDT)
 +
   
 +
    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
 +
    VNTR Summary
 +
    rid          : 19
 +
    motif        : AC
 +
    ru          : CA
 +
   
 +
    Exact
 +
    repeat_tract                    : CACACACACACACACA
 +
    position                        : [131949,131964]
 +
    reference repeat unit length    : 8
 +
    longest allele length          : 4.55884e-41
 +
    motif_concordance              : 1
 +
    repeat units                    : 8
 +
    exact repeat units              : 8
 +
    total no. of repeat units      : 8
 +
   
 +
    Fuzzy
 +
    repeat_tract                    : CACCACACACACACACACA
 +
    position                        : [131946,131964]
 +
    reference repeat unit length    : 19
 +
    longest allele length          : 0
 +
    motif_concordance              : 0.95
 +
    repeat units                    : 19
 +
    exact repeat units              : 9
 +
    total no. of repeat units      : 10
 +
    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
    
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Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/13783"

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