dme-mir-3642

dme-mir-3642

Changes
- One base within the D. simulans mature region was flagged as a possible genomic error. Upon resequencing, we confirmed this base is indeed a genomic error, and uncovered two additional gaps within the mature region that are also errors.
- D. simulans star sequence contain three ambiguous bases (see below). In all instances, the base reported in the reference assemblies agree with the resequencing results.

Species	Chrom	Pos	Ref base	Type	A	C	G	T	RNAseq Total	A	C	G	T	Trace Total	Decision	Partition
droSim1	chr3L	10995124	G	3	0	0	0	0	0	0	0.909	0.091	0	11	Resequencing supports genomic error	miR
droSim1	chr3L	10995153	A	3	0	0	0	0	0	0.182	0.818	0	0	11	Ambiguous - Other simulans lines support 'C' reference base but resequencing supports the 'A' allele	miR*
droSim1	chr3L	10995177	C	3	0	0	0	0	0	0	0.154	0.154	0.692	13	Ambiguous - Other simulans lines support 'T' reference base but resequencing supports the 'C' allele	miR*
droSim1	chr3L	10995184	A	3	0	0	0	0	0	0.167	0.833	0	0	12	Ambiguous - Other simulans lines support 'C' reference base but resequencing supports the 'A' allele	miR*

Corrected alignment

dme-mir-3642

Species	Coordinate	Alignment
dm3	chr3L:11622590-11622695 +	ATGGATGACGTCAAGGTGAGTG--------------GGTCGCACGGAGCGTCATT-------------------------TGGAAT-------------------TC------------CCATGGC-------TG------ACGAA-------------------ACGTTCACTCTGCTCTTCTCGATTACAGGACATCATCAGTAAA
droSim1	chr3L:10995092-10995212 +	ATGGATGACGTCAAGGTGAGTG--------------AGGCGCACGGAGCGCCATT-------------------------TGGAAT-------------------TC------------CCCTGGC-------TG------AGAAAACGCTA--AGAACTTCATTACGCTCACTCTGTTATTCTCGATTACAGGACATCATCAGTAAA
droSec1	super_0:3809862-3809984 +	ATGGATGACGTCAAGGTGAGTG--------------AGGCGCACGGAGCGTCATT-------------------------TGGAAT-------------------TC------------CCCTGGC-------TG------AGAAAACGCTA--AGAACTTCATTACGCTCACTCTGTTCTTCTCGATTACAGGACATCATCAGTAAA
droYak2	chr3L:11651195-11651318 +	ATGGATGACGTCAAGGTGAGTG--------------CGGCGCACGAACCGCCATT-------------------------TGGAAT-------------------TC------------CCCTGGC-------TG------ACGAAACGCTAA-AGAACTTCATTACGCTCACTCTGCTCTTTTCAATTACAGGACATAATCAGTAAA
droEre2	scaffold_4784:11607138-11607238 +	ATGGATGACGTCAAGGTGAGTG--------------AGGCGCACGGACCGCCATT-------------------------TCGAAT-------------------TC------------CCCTGTC-------TG------------------------------ACGCTCACTCTGCTCTTTTCAATTACAGGACATAATCAGTAAA
droAna3	scaffold_13337:5894397-5894534 +	ATGGACGACGTCAAGGTGAGTAAGAAGTGGTGGAGGGGGTGT------------------TGCAG------CAAAGTGC-TGGAAC-------------------TT------------AATAAGC-------TA------ATGAAACGCTAA-AGAACTTCATTACCCTTTCTTTGCTCTTTTCAATTACAGGACATAATCAGTAAA
dp4	chrXR_group6:10064193-10064317 -	ATGGACGACGTGAAGGTGAGTG--------------GGGCGC------------------TGCAC------GTGCCCGCTTGAGAC-------------------TT------------GCTTGGC-------AA------TATCAACGCTAA-AGAACTTCATTACGCTCATTATGCTCTTCTCCATTGCAGGACATAATCAGTAAA
droPer1	super_61:344655-344779 -	ATGGACGACGTGAAGGTGAGTG--------------GGGCGC------------------TGCAC------GTGTCCGCTTGAGAC-------------------TT------------GCTTGGC-------AA------TATCAACGCTAA-AGAACTTCATTACGCTCATTATGCTCTTCTCCGTTGCAGGACATAATCAGTAAA
droWil1	scaffold_180698:2114822-2114981 +	ATGGACGACGTAAAGGTGAGTG--------------TAACA--------------------GCACTAGTGTGTGTACGCCTGTGC-GTGTGTGTGTGTGTGTGTGCGTATATTT-----TCATGTA-------ATTATCCAACG-ACCGCTAATAGAATTTCCTTACACTTACTTTGCTCTTCTCACTTGCAGGACATAATCAGTAAA
droVir3	scaffold_13049:23825799-23825928 +	ATGAATGATGTCAAGGTGAGTG--------------CGCGGCGCGGCGGCTGCTT-----------------------CTTAATAA-------------------TT--------GATG-------AATTGACAA------TCTTATCGTTAA-AGAATTTCCTTACTCTCTGTCTGCTCTTATCTCTTACAGGACATAATCAGTAAA
droMoj3	scaffold_6680:18448682-18448807 +	ATGAACGACGTGAAGGTGAGTG--------------AGCGGAATG-----C---------TGAAC----------------------------------------TGAATTTATTGATG-------AATTGACAA------TCTTATCGTTAA-AGAATTTCATTACACTCTCCTTGCTCTTCTCTCTTGCAGGACATAATCAGTAAA
droGri2	scaffold_15110:13832957-13833097 -	ATGAGCGATGTAAAGGTGAGTT--------------CGGA-------GCGTTATTCTAGTTGATT------GTGTTTAATTTTTAT-------------------AT------------ATTTGGCAATTGTTAA------TCAATTCGTTAA-AGAATTTCCT--CACTCACTCTGCTCTTATCTCTTCCAGGACATAATCAGTAAA