deCIPher
Sample Information Sequencing data Molecular Characterization Homology Insertion Site1

Report - Basic Information

Sample Information

SpeciesRice
Genome Size385.7 Mb
Chromosome Count12
Insert Gene Size19909
Project IDa78f0cd2-1e3f-4119-8674-12cef5cbf06c
Submission Time2024-10-23 06:21:46
Report Time2024-10-23 06:22:10
Runtime24.19s

Diagram of chromosomes

Sequencing Data

Sequencing TypeIllumina
Pre QC Size16.74 GB
Post QC Size15.92 GB
Coverage199.83%
Coverage1090.86%
Coverage Half Depth84.60%

Diagram of coverage distribution

coverage_distribution

Molecular Characterization

Genome Depth27.62
Genome Standard Deviation93.33
T-DNA Depth77.54
T-DNA Standard Deviation57.83
T-DNA Copy Number2.807

Backbone Residue

residue

Report - Insertion Sites

Homologous Analysis

Top 10 BLAST Alignments

Number Chromosome Genome Start Genome End T-DNA Start T-DNA End Score Identity (%) Alignment Length
1 >NC_029263.1 1751267 1755698 6 4435 8133.0 99.8% 4432
2 >NC_029263.1 23341662 23342600 9341 10284 1140.0 88.57% 945
3 >NC_029263.1 23335527 23336467 9338 10284 813.0 82.33% 951
4 >NC_029263.1 23342690 23342979 10286 10574 340.0 87.93% 290
5 >NC_029263.1 11675357 11675393 6578 6614 63.9 97.3% 37
6 >NC_029263.1 18228111 18228145 6578 6612 60.2 97.14% 35
7 >NC_029263.1 19249052 19249086 6580 6614 60.2 97.14% 35
8 >NC_029263.1 19993743 19993709 6580 6614 60.2 97.14% 35
9 >NC_029263.1 25172302 25172336 6578 6612 60.2 97.14% 35
10 >NC_029263.1 23060578 23060546 6580 6612 56.5 96.97% 33
11 >NC_029264.1 17296364 17297304 9339 10285 774.0 81.6% 951
12 >NC_029264.1 17303561 17304502 9338 10285 749.0 81.13% 954
13 >NC_029264.1 17289901 17290707 9472 10284 704.0 82.52% 818
14 >NC_029264.1 329737 329699 6578 6616 67.6 97.44% 39
15 >NC_029264.1 3544404 3544370 6578 6612 60.2 97.14% 35
16 >NC_029264.1 4124932 4124966 6578 6612 60.2 97.14% 35
17 >NC_029264.1 8549020 8549054 6580 6614 60.2 97.14% 35
18 >NC_029257.1 32243622 32244416 9472 10266 477.0 77.87% 809
19 >NC_029257.1 32249703 32248891 9472 10284 466.0 77.44% 829
20 >NC_029257.1 10845666 10845629 6578 6615 65.8 97.37% 38
21 >NC_029257.1 11454867 11454903 6578 6614 63.9 97.3% 37
22 >NC_029257.1 14187638 14187674 6578 6614 63.9 97.3% 37
23 >NC_029257.1 22034884 22034848 6578 6614 63.9 97.3% 37
24 >NC_029257.1 8339488 8339454 6580 6614 60.2 97.14% 35
25 >NC_029257.1 11993414 11993380 6580 6614 60.2 97.14% 35
26 >NC_029257.1 14633134 14633168 6578 6612 60.2 97.14% 35
27 >NC_029261.1 30264909 30265716 9471 10269 425.0 76.56% 815
28 >NC_029261.1 22601234 22601327 3523 3616 152.0 95.74% 94
29 >NC_029261.1 22601334 22601445 4013 4129 111.0 84.75% 118
30 >NC_029261.1 4551208 4551244 6578 6614 63.9 97.3% 37
31 >NC_029261.1 10076015 10075979 6578 6614 63.9 97.3% 37
32 >NC_029261.1 15107887 15107851 6578 6614 63.9 97.3% 37
33 >NC_029261.1 15690232 15690196 6578 6614 63.9 97.3% 37
34 >NC_029261.1 13218555 13218589 6580 6614 60.2 97.14% 35
35 >NC_029261.1 25469052 25469018 6580 6614 60.2 97.14% 35
36 >NC_029266.1 12123278 12123478 19698 19898 372.0 100.0% 201
37 >NC_029266.1 984590 984554 6578 6614 63.9 97.3% 37
38 >NC_029266.1 5300120 5300154 6580 6614 60.2 97.14% 35
39 >NC_029266.1 11307199 11307165 6580 6614 60.2 97.14% 35
40 >NC_029266.1 18522870 18522904 6580 6614 60.2 97.14% 35
41 >NC_029266.1 23531154 23531122 6580 6612 56.5 96.97% 33
42 >NC_029266.1 12123517 12123545 6314 6342 54.7 100.0% 29
43 >NC_029256.1 14460643 14461126 9759 10235 217.0 75.65% 497
44 >NC_029256.1 14007693 14007657 6578 6614 63.9 97.3% 37
45 >NC_029256.1 18433960 18433923 6578 6615 60.2 94.74% 38
46 >NC_029259.1 8837559 8837598 6578 6617 69.4 97.5% 40
47 >NC_029259.1 9495261 9495223 6578 6616 67.6 97.44% 39
48 >NC_029259.1 20535403 20535366 6578 6615 65.8 97.37% 38
49 >NC_029259.1 1517544 1517508 6578 6614 63.9 97.3% 37
50 >NC_029259.1 20179642 20179678 6578 6614 63.9 97.3% 37
51 >NC_029259.1 28939832 28939868 6578 6614 63.9 97.3% 37
52 >NC_029259.1 6864083 6864046 6578 6615 60.2 94.74% 38
53 >NC_029258.1 19833336 19833375 6578 6617 69.4 97.5% 40
54 >NC_029258.1 20296888 20296849 6578 6617 69.4 97.5% 40
55 >NC_029258.1 8292643 8292609 6580 6614 60.2 97.14% 35
56 >NC_029258.1 18810512 18810546 6580 6614 60.2 97.14% 35
57 >NC_029265.1 2643010 2643048 6578 6616 67.6 97.44% 39
58 >NC_029265.1 12368066 12368103 6578 6615 65.8 97.37% 38
59 >NC_029265.1 5653975 5654011 6578 6614 63.9 97.3% 37
60 >NC_029265.1 24810 24844 6578 6612 60.2 97.14% 35
61 >NC_029262.1 11307227 11307190 6578 6615 65.8 97.37% 38
62 >NC_029262.1 16582243 16582207 6578 6614 63.9 97.3% 37
63 >NC_029262.1 6194847 6194810 6578 6615 60.2 94.74% 38
64 >NC_029262.1 8983504 8983470 6580 6614 60.2 97.14% 35
65 >NC_029262.1 19819640 19819606 6580 6614 60.2 97.14% 35
66 >NC_029262.1 22746948 22746914 6580 6614 60.2 97.14% 35
67 >NC_029262.1 11859472 11859440 6580 6612 56.5 96.97% 33
68 >NC_029260.1 9090197 9090160 6578 6615 65.8 97.37% 38
69 >NC_029260.1 4358060 4358026 6578 6612 60.2 97.14% 35
70 >NC_029260.1 15107760 15107726 6580 6614 60.2 97.14% 35
71 >NC_029267.1 15351073 15351107 6580 6614 60.2 97.14% 35
72 >NC_029267.1 16242049 16242015 6580 6614 60.2 97.14% 35
Homology Value = Total Aligned Bases T-DNA Length × 100 %

TDNA BLAST Frequency

tdna_depth

Insertion Region:('chromosome_4', 25339444, 25340686)

Specific Positionchromosome_4: 25340065
Site in T-DNA17514
Directionforward
Order of BoundaryUpstream
Unexpected Small Insertion-3 bp
Full Sequence of Small InsertionNone

Diagram of insertion site

insertion_site1-1

Flanking sequences:

( genome sequence    T-DNA sequence)
AAGCTCAGTTCTCACGGATTAGAAATAGATTTATCTAAATGCATGATCAATCTATTAGTATGTAGTACCCACAAAGTTTCGAGATTCCAAAAATATACCCCACCGCCGCGCCGGACTCCAAAATCCCTACCATTCGGATGTGTATTCTGGGCCACGAACGTGACAACGCCTACTATACAATGCCATTACCAAAACCAACAAACCGCCTATACAGCAGCAGCAGCAAAAGGCAGCAAATGCCCGGGGGGTGCGAAGGAAGCTCACAGCGCGGGGAGCGGGGAGCAGCGAGGGCGGTGGCGGCGCCGGAGAAACGAGTCGGCGGCGACGGGAAGCCACCGCGGCGTGGCGGCCACGAGCGAGCTCGCGAGCAGCCGCTGAATGGCCATGGCGCCGCCCGGCGCGCGGGGAGGGGGAGGAGACCCGCCGCCGCTAGGGTTCCAGCCTTCCGGTGGCTCCCCGGCCCGCGGAGCGCCTGGCTCCGGCCGCCTCCGTGGACGCCGGCGGAATGAGACCGGCGGCCCACCGCCACCGCGAGGGTTTTGGGGGAAGCGAGGAGCGGAGAAGAGGAGAGAGATATGGGCGGTTTGGGGTTTTGGGAAGTGTCAGGGCGCGAGCAGCCAAGAGGCGGTGTGGGGTTGTGGTTGT AAACAAATTGACGCTTAGACAACTTAATAACACATTGCGGACGTTTTTAATGTACTGAATTAACGCCGAATTAATTCGGGGGATCTGGATTTTAGTACTGGATTTTGGTTTTAGGAATTAGAAATTTTATTGATAGAAGTATTTTAAAAATAAAAATAAATACTAATGGTTTCTTATATGCTCAAA


Specific Positionchromosome_4: 25340082
Site in T-DNA7496
Directionforward
Order of BoundaryDownstream
Unexpected Small Insertion-4 bp
Full Sequence of Small InsertionNone

Diagram of insertion site

insertion_site1-2

Flanking sequences:

( genome sequence    T-DNA sequence)
AACAATCGAACACACTTGAACAAACATTAGTCGTAGCCTCGTAAGAGATATGATCAACGTTATACAAATGAGCTATGTGTGTTATGTTTCAATCAAAGTTTCGAGAATCAAGAATATTTAGCTCATTCCTAAGTTTGCTAAAGGTTTTATCATATAATGGTTTGGTAAAGATATCGACTAATTG TTCTCGGGGTAGTGCGCACACGTCCCGACGTGACGTGACTGATGGGTGGGCCATGGTTTCACGGGCTCACGGTCCATGGGCTTTTTGTATTCTGGGCTGGCTGAACAACCTCAGGTTGTTTAAGCTGTCTGATTGTTTGCATTTAGCGCCTGATAAAAAGACCAGGCGACTACAGTATCATTACCCCCATGGTCCAGTGTTCCATCAGATTTGTCACGGTTCGTATATATATTCAAAAATAAAATAAAATGGAGAAGCCTACCACGGAAAAAGCGATCTTTGACACAGGATTCTCGTTAATAATCAAGTCACGTAGGCTGCAAAACAACATGTACATGGGCACATGGCATATCACATTCACTTGGGCGATGTCGCTGGGATGCAGGAAGCAAAATCAACCCCACAGAAGTTAAAGCAATCATCAAACTCTTCCTGTTCTTGTTCTAGTATAAGCTATAGATCGAACCCGGCCGTCCTTTTTTTTCTCCAATCAACTAATGTTTTCACGGTCTGTATCAGTCAAATATTCAAAGCACCCTCCCGTCCATCCCATCAAGGAGGCCGGACCACATCCCCTTCACCGGCGGCAGCTGCGCCACGAACGCTTGCCACGGCGGGTACCCGACGCCGCTGCCACGGACGC