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first draft of next version
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lpantano committed Oct 24, 2018
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5 changes: 5 additions & 0 deletions Changes.md
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# 1.1 October, 24th, 2018

* UID is following exactly MINTplates licenses since this commit: 7f7717d5f23ea638f1a14fccc6386e1dbb8a7e1a in mirtop applied
* iso_5p and iso_3p changed their meaning. Nows the sign means whether the isomiR starts or ends upstream or downstream the refence sequence.
* SNP was change to SNV to support any kind of variant
18 changes: 9 additions & 9 deletions definition.md
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**Version**

VERSION: 1.0
VERSION: 1.1

**Description**

Expand Down Expand Up @@ -35,25 +35,25 @@ Please add description for each columns/attribute (R:required, O:optional)
* (R) column4/5: start/end: precursor start/end as indicated by alignment tool
* (O) column6: score (Optional): It can be the mapping score or any other score the tool wants to assign to the sequence.
* (R) column7: strand. In the case of mapping against precursor should be always `+`. It should accept mapping against the genome: `+/-` allowed.
* (O) column8: phase: (For features of type "CDS", the phase indicates where the feature begins with reference to the reading frame): Not relevant righ now. This can be: `.`
* (O) column8: phase: (For features of type "CDS", the phase indicates where the feature begins with reference to the reading frame): Not relevant right now. This can be: `.`
* (R) column9: attributes:
* (R) UID: unique ID based on sequence like mintmap has for tRNA: prefix-22-BZBZOS4Y1 (https://github.com/TJU-CMC-Org/MINTmap/tree/master/MINTplates). good way to use it as cross-mapper ID between different naming or future changes. Currently supported by [mirtop](https://github.com/miRTop/mirtop/blob/dev/mirtop/mirna/realign.py#) code.
* (R) UID: unique ID based on sequence like MINTplates has for tRNA: prefix-22-BZBZOS4Y1 (https://github.com/TJU-CMC-Org/MINTmap/tree/master/MINTplates). It is a good way to use it as cross-mapper ID between different naming or future changes. Currently supported by [mirtop](https://github.com/miRTop/mirtop/blob/dev/mirtop/mirna/realign.py#) code.
* (O) Read: read sequence
* (R) Name: mature name
* (R) Parent: hairpin precursor name
* (R) Variant: (categorical types - adapted from isomiR-SEA)
* `iso_5p:+/-N`. `+` indicates extra nucleotides not in the reference miRNA. `-` indicates removed nucleotides not in the sequence. `N` the number of nucleotides of difference. For instance, if the sequence starts 2 nts after the reference miRNA, the label will be: `iso_5p:-2`, but if it starts before, the label will be `iso_5p:+2`.
* `iso_3p:+/-N`. Same explanation applied.
* `iso_add:+N`. Same explanation applied.
* `iso_snp_seed`: when affected nucleotides are between [2-7].
* `iso_snp_central_offset`: when affected nucleotides is at position [8].
* `iso_snp_central`: when affected nucleotides are betweem [9-12].
* `iso_snp_central_supp`: when affected nucleotides are betweem [13-17].
* `iso_snp`: anything else.
* `iso_snv_seed`: when affected nucleotides are between [2-7].
* `iso_snv_central_offset`: when affected nucleotides is at position [8].
* `iso_snv_central`: when affected nucleotides are between [9-12].
* `iso_snv_central_supp`: when affected nucleotides are between [13-17].
* `iso_snv`: anything else.
* (O) Changes (optional): similar to previous one but indicating the nucleotides being changed.
* additions are in capital case
* deletions are in lower case
* example: `Changes iso_5p:0,iso_3p:TT,iso_add:GTC` where `Variant iso_add:+3,iso_3p:-2`.
* example: `Changes iso_5p:0,iso_3p:TT,iso_add:GTC` where `Variant iso_add:+3,iso_3p:+2`.
* (R) Cigar: CIGAR string as indicated [here](https://samtools.github.io/hts-specs/SAMv1.pdf). It is the standard CIGAR for aligners. With the restriction that `M` means exact match always. That's a difference with some aligners where `M` includes mismatches. In this case, if there is a mismatch, then it should be output like: `11MA7M` to indicates there is a mismatch at position 12, where `A` is the reference nucleotide.
* (R) Hits: number of hits in the database.
* (O) Alias (Optional): get names from miRBase/miRgeneDB or other database separated by `,`
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71 changes: 15 additions & 56 deletions example.gff
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## GFF3 adapted for miRNA sequencing data. VERSION 1.0
## source-ontology: miRBase v21 doi:10.25504/fairsharing.hmgte8
## COLDATA: reads
hsa-let-7a-1 miRBasev21 isomiR 4 26 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_5:27_-1:0_mut:null_add:null_x103; UID=bhJJ5WJQ1; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:+1; Cigar=23M; Expression=103; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 4 25 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:null_add:null_x861; UID=bhJJ5WJL2; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:+1,iso_3p:-1; Cigar=22M; Expression=861; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 4 26 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_5:27_-1:0_mut:18C_add:null_x198; UID=bhJJ5YJQ1; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snp_central_supp,iso_5p:+1; Cigar=17MC5M; Expression=198; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 4 25 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:11C_add:null_x8; UID=bhJP5WJL2; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snp_central,iso_5p:+1,iso_3p:-1; Cigar=10MC11M; Expression=8; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 4 27 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:null_add:TA_x5; UID=bhJJ5WJQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+1,iso_5p:+1; Cigar=23MA; Expression=5; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 4 26 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_5:27_-1:0_mut:11G_add:null_x8; UID=bhJu5WJQ1; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snp_central,iso_5p:+1; Cigar=10MG12M; Expression=8; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 4 27 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:1T_add:TT_x290; UID=RhJJ5WJ%; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snp,iso_5p:+1,iso_3p:+1; Cigar=T23M; Expression=290; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 4 25 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:10C_add:null_x66; UID=bhJD5WJL2; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snp_central,iso_5p:+1,iso_3p:-1; Cigar=9MC12M; Expression=66; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 4 27 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_5:26_-1:-1_mut:3T_add:TA_x11; UID=phJJ5WJQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snp_seed,iso_add:+1,iso_5p:+1; Cigar=2MT20MA; Expression=11; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 25 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:null_x0; UID=7AwhRzw; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:-1; Cigar=21M; Expression=0; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 27 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:AT_x713; UID=7AwhRzwg1; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+2,iso_3p:-1; Cigar=21MAM; Expression=713; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 28 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:TTT_x116; UID=7AwhRzw%; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:+2; Cigar=24M; Expression=116; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 25 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:8C_add:null_x13; UID=7AshRzw; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snp_seed,iso_3p:-1; Cigar=7MC13M; Expression=13; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 28 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:TAT_x152; UID=7AwhRzwz; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+2; Cigar=22MAM; Expression=152; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 29 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_6:27_0:0_mut:null_add:ATT_x32; UID=7AwhRzwzL2; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snp,iso_3p:+2; Cigar=22MI2M; Expression=32; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 25 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:6A_add:null_x24; UID=7KwhRzw; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snp_seed,iso_3p:-1; Cigar=5MA15M; Expression=24; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 28 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_6:27_0:0_mut:null_add:TA_x8; UID=7AwhRzwQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+1,iso_3p:+1; Cigar=23MA; Expression=8; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 27 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:TT_x103; UID=7AwhRzwQ1; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:+1; Cigar=23M; Expression=103; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 27 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:6G_add:TA_x58; UID=7$whRzwL1; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snp_seed,iso_add:+1; Cigar=5MG16MA; Expression=58; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 29 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_6:27_0:0_mut:null_add:TTT_x41; UID=7AwhRzw%L2; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+1,iso_3p:+2; Cigar=24MT; Expression=41; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 ref_miRNA 5 26 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_6:27_0:0_mut:null_add:null_x4; UID=7AwhRzwL2; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=NA; Cigar=22M; Expression=4; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 27 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:TA_x11; UID=7AwhRzwL1; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+1; Cigar=22MA; Expression=11; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 26 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_6:26_0:-1_mut:null_add:A_x550; UID=7AwhRzw@2; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+1,iso_3p:-1; Cigar=21MA; Expression=550; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 6 27 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:null_add:AT_x693; UID=4WWABgWL2; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+2,iso_5p:-1,iso_3p:-1; Cigar=20MAM; Expression=693; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 6 26 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_7:27_1:0_mut:null_add:null_x37; UID=4WWABg5; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-1; Cigar=21M; Expression=37; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 6 25 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:null_add:null_x0; UID=4WWABgW1; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-1,iso_3p:-1; Cigar=20M; Expression=0; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 6 28 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:null_add:TAT_x15; UID=4WWABg5g1; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+2,iso_5p:-1; Cigar=21MAM; Expression=15; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 6 26 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:11T_add:T_x29; UID=4WW5Bg5; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snp_central,iso_5p:-1; Cigar=10MT10M; Expression=29; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 6 28 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:null_add:TAA_x9; UID=4WWABg5@1; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+2,iso_5p:-1; Cigar=21MAA; Expression=9; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 6 29 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_7:27_1:0_mut:null_add:TTA_x280; UID=4WWABg5Q; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-1,iso_3p:+3; Cigar=24M; Expression=280; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 6 28 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_7:26_1:-1_mut:null_add:AAA_x41; UID=4WWABgW@1; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+3,iso_5p:-1,iso_3p:-1; Cigar=20MAAA; Expression=41; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 6 29 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_7:27_1:0_mut:null_add:TAT_x543; UID=4WWABg5z; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+2,iso_5p:-1,iso_3p:+1; Cigar=22MIM; Expression=543; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 7 28 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:null_add:AAA_x0; UID=hJJ5WJL@2; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+3,iso_5p:-2,iso_3p:-1; Cigar=19MAAA; Expression=0; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 7 25 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:18A_add:null_x59; UID=hJJ5WLL2; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+2,iso_5p:-2,iso_3p:-3; Cigar=17MAM; Expression=59; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 7 26 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_8:27_2:0_mut:null_add:null_x108; UID=hJJ5WJQ1; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-2; Cigar=20M; Expression=108; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 7 29 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_8:27_2:0_mut:null_add:TTA_x1001; UID=hJJ5WJ%L1; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-2,iso_3p:+3; Cigar=23M; Expression=1001; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 7 25 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:9C_add:null_x6; UID=hJN5WJL2; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snp_central_offset,iso_5p:-2,iso_3p:-1; Cigar=8MC10M; Expression=6; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 7 28 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:null_add:AAT_x40; UID=hJJ5WJLL2; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+3,iso_5p:-2,iso_3p:-1; Cigar=19MAAM; Expression=40; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 7 26 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:2T_add:T_x20; UID=bJJ5WJQ1; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snp,iso_5p:-2; Cigar=MT18M; Expression=20; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 7 25 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:null_add:null_x1; UID=hJJ5WJL2; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-2,iso_3p:-1; Cigar=19M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 7 27 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_8:26_2:-1_mut:18A_add:TA_x51; UID=hJJ5WLQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snp_central_supp,iso_add:+1,iso_5p:-2; Cigar=17MA2MA; Expression=51; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 8 26 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:null_add:A_x239; UID=AwhRzw@2; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+1,iso_5p:-3,iso_3p:-1; Cigar=18MA; Expression=239; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 8 25 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:10A_add:null_x48; UID=Awhbzw; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snp_central,iso_5p:-3,iso_3p:-1; Cigar=9MA8M; Expression=48; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 8 25 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:14G_add:null_x29; UID=AwhRBw; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snp_central_supp,iso_5p:-3,iso_3p:-1; Cigar=13MG4M; Expression=29; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 8 28 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_9:27_3:0_mut:null_add:AT_x246; UID=AwhRzwz; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+2,iso_5p:-3; Cigar=19MAM; Expression=246; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 8 26 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_9:27_3:0_mut:2T_add:null_x0; UID=5whRzwL2; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snp,iso_5p:-3; Cigar=MT17M; Expression=0; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 8 27 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:null_add:TA_x576; UID=AwhRzwL1; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+1,iso_5p:-3; Cigar=19MA; Expression=576; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 8 26 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_9:27_3:0_mut:null_add:null_x103; UID=AwhRzwL2; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-3; Cigar=19M; Expression=103; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 8 25 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:6A_add:null_x4; UID=AmhRzw; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snp_seed,iso_5p:-3,iso_3p:-1; Cigar=5MA12M; Expression=4; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 8 27 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_9:27_3:0_mut:null_add:T_x16; UID=AwhRzwQ1; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-3,iso_3p:+1; Cigar=20M; Expression=16; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 8 25 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:18C_add:null_x2; UID=AwhRzk; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+1,iso_5p:-3,iso_3p:-2; Cigar=17MC; Expression=2; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 8 25 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:null_add:null_x508; UID=AwhRzw; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-3,iso_3p:-1; Cigar=18M; Expression=508; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 8 27 0 + . Read=hsa-let-7a-1_hsa-let-7a-5p_9:26_3:-1_mut:4T_add:TT_x616; UID=ABhRzwQ1; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snp_seed,iso_5p:-3,iso_3p:+1; Cigar=3MT16M; Expression=616; Filter=Pass; Hits=1
## mirGFF3. VERSION 1.1
## source-ontology: miRBasev21 doi:10.25504/fairsharing.hmgte8
## COLDATA: let7a-5p
hsa-let-7a-1 miRBasev21 isomiR 3 26 0 + . Read=GATGAGGTAGTAGGTTGTATAGTT; UID=iso-24-5URPV39QFE; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-2; Cigar=24M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 4 26 0 + . Read=ATGAGGTAGTAGGTTGTATAGTT; UID=iso-23-I0S31NSL0E; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:-1; Cigar=23M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 26 0 + . Read=TGAGGTAGTACGTTGTATAGTT; UID=iso-22-XKVLMYVPQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_snv_central; Cigar=10MC11M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 28 0 + . Read=TGAGGTAGTAGGTTGTATAGTTAA; UID=iso-24-XKVLRYVPKF; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+2; Cigar=22MAA; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 27 0 + . Read=TGAGGTAGTAGGTTGTATAGTTT; UID=iso-23-XKVLRYVP0Q; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:+1; Cigar=23M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 24 0 + . Read=TGAGGTAGTAGGTTGTATAG; UID=iso-20-XKVLRYVP; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:-2; Cigar=20M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 28 0 + . Read=TGAGGTAGTAGGTTGTATAGTTTT; UID=iso-24-XKVLRYVPKQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:+2; Cigar=24M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 25 0 + . Read=TGAGGTAGTAGGTTGTATAGT; UID=iso-21-XKVLRYVPE; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_3p:-1; Cigar=21M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 5 27 0 + . Read=TGAGGTAGTAGGTTGTATAGTTA; UID=iso-23-XKVLRYVP0O; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_add:+1; Cigar=22MA; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 ref_miRNA 5 26 0 + . Read=TGAGGTAGTAGGTTGTATAGTT; UID=iso-22-XKVLRYVPQ; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=NA; Cigar=22M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 6 26 0 + . Read=GAGGTAGTAGGTTGTATAGTT; UID=iso-21-531P7WH3E; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:+1; Cigar=21M; Expression=1; Filter=Pass; Hits=1
hsa-let-7a-1 miRBasev21 isomiR 7 26 0 + . Read=AGGTAGTAGGTTGTATAGTT; UID=iso-20-1LSKZLVN; Name=hsa-let-7a-5p; Parent=hsa-let-7a-1; Variant=iso_5p:+2; Cigar=20M; Expression=1; Filter=Pass; Hits=1

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