Question about different mappings of same read

[nadjano]

Hello,

I am mapping a set of reads to two different references consisting of gene regions.
The same read maps in both genomes to the same gene, but with different AS and NM scores, even though the reference sequence is identical.
I suspect this is related to that the indices of the references are different, as not all genes are exactly identical.

Is there a way to resolve this? And get same mapping scores in the two alignments. Or is there better scores to look at than AS or NM to compare two alignments?

Thank you for your help! :)

Best,
Nadja

minimap2 \
                -t 32 \
                -a \
                -u f \
                -x splice \
                --secondary=no \
                -C 5 \
                ref.fasta \
                red.fq \
                > sam

i already tried --no-long-join

fl_rsc_dm12279_01h_rep1_TR4_2_dm12279_upd_gene_plusMinus100.sam:106:1299|786a24f5-e82a-4125-ade8-3af86e75d068	16	FBgn0013686	106	60	2S46M1I22M1D61M1I21M1I28M2D3M1D35M2I7M2D339I81M1D21M1I65M1D397M1D22M2I33M2S	*	0	0	ACATTAATAGTATTCTTATAAAAAATATAATTATTTTGATATTTGGTCACTTTCGTACTAAAATATCACAATTTTTAAAGATAGAAACCAACCTGGCTTACACCGGTTTGAACTCAGATCATGTAAGAATTTAAAAAGTCGAACAGACTTAAAATTTTGAACGGCTACACCCAAAATTATATCAATCAACATCGAGGTCGCAATCTTTTTTATCGATATGAAGACTCTCCAAAAATTACGCTGTTATCCCTGAAAATGACACAATTTTTTAAAGCTTAAATTTATGAATATTTGATCCATTAATAATGATTAAAAAATTAAGTTACTTTAGGGATAACAGCGTAATTTTTGGAGAGTTCATATCGATAAAAAAGATTGCGACCTCGATGTTGGATTAAGATATAATTTTGGGTGTAGCCGTTCAAATTTTAAGTCTGTTCGGCAAATTCTTACATGATCTGAGTTCAAAACAAACCAAAAAGTCGAACAGACTTAAAATTTGAACAGCTACACCATTATAACTTAATCCAACATCGAGGTCGCAATCTTTTTTTATCGATATAAGTCTCAAAAATTACGCTGTTATCCCTAAAGTAACTTAATTTTTTAATCATTATTAATGGATCAAATATTCATAAATTTATGTTTTTAAAAATTAAAAGTTTTTTAAATTTTTAATATCACCCCAATAAAATATTTTTATTTATTAAAATTTAATTAATCTATATAATTAAAATAAAAAAAATATAAAGATTTATAGGGTCTTCTCGTCTTTTAAATAAATTTTAGCTTTTTGACTAAAAAATAAAATTCTATAAAAATTTTAAATGAAACAGTTAATATTTCGTCCAACCATTCATTCCAGCCTTCAATTAAAAGACTAATGATTATGCTACCTTTGCACTGTCAAAATACTGCGGCCATTTAAAATTTTCAGTGGGCAGGTTAGACTTTATATATAATTCAAAAAGACATGTTTTTGTTAAACAGGCGAATATTATTTTTGCCGAATTCTTTATTTAAACTTTTCATATAAATTAATTTTAACATTATTATATACTAATTTTATCATTATTGCTTAATTTTAATAATTAAAACTAACATTTTAATAAATAATTAAAATTTAATAAATAATTAATTTATAAAATAAATTATAACACACATTTTTTAATAATTGCTAATTCTAAGCATCC	:G>S:SJELGHSSSSIEIHHSJJSJCGASGPHSHLDCCH9KFBKFD=B.---2/<8IKSHHSKGM>FFLSFFSSCIKI8496>AEHI6E<CDCI?5444@B?KISSAHHLK@G<JSFKKGSMSSJ8:AABIKFCSALGS<H:SEAGJ@HIDSS:SGB88QGSQSSHJIOQHLISSEG>MEG430,,2969EFLJNRNISMKMDL@HPSNSBHF4F987677)(''''00/,+,-.3//8LNGSSKGSDSC==9976/....--.//>LD@D<9AC>9437?ALSSJGFSHMKSSHG<KSSDSI@@@@AHQES>AB2).B5C:HGHIGLK?>1H@LPBCAA@@ASGJHM=OO8MESS=JMJGFI<SFJECQGLEGD8311189BFOSSSJLIFSEHKGCHJGSHSKGKR<LNFCGSPFHINSR@D786620000029A??422/+))*?C=9ADEN@=BIMEESDFJC?A')++-..+*+0-.4=OF>HFKIFKE?BSCHKSHKJJFJKH6510,,,,.36@KEGSFAHC@BEKSEEAA1001FBIS:HIOSM<;;>13D@B?(&&&()*(((-5CC9@<<<<<LQFIGS+10K788:99899:;@:967968;HEGCBA?AAB@A<CSABCDDD?CBEGD@HCFGHFHEIG32789078;./210;?14/48<==:=@=>GGDDC@??>A?CDFCDECCAA1/.//2ACCR>D15;:;<;=B@@@@AEFDCCGFIAD?;ABA;5145AEGS>32223A@436:<>B.,,,-../C@E764@>;:;>=D?<BABECCF>99888>:D>=E?AABBBCCFB=<7556>31;DACCCC:AAACGHMIEB=<;4347?@@ACC?B>...3779BBCCGHNHGSH?:?CACDCDGF@<<<<=CCBDSFE=BBABCBKE<;:5449:;;??>>A=@JB@@E411002=:9888:79997=7>??=@??AASECF*)*,5>>@@BBEAD<4>GD5333334:;;@EDBBA>>C>?:::;;CCBAB@=>=?=;=>>EMG?MKSSRDGAKA@S6:HDDDFDEEHHHC97.-,4>ABIDDDBB>=</+*****,//248A@@>>>;<>=>>=BDCC<0/.3BKEEAFGJSD14BDC@=<?A=:776('))7099;==?>ADABBBJFE760//01<1/,/-/=BCBBBB===>B@>>65555/	NM:i:361	ms:i:594	AS:i:752	nn:i:0	ts:A:+	tp:A:P	cm:i:223	s1:i:732	s2:i:185	dv:f:0.0401
fl_rsc_dm12279_01h_rep1_TR4_2_w1118_upd_gene_plusMinus100.sam:106:1299|786a24f5-e82a-4125-ade8-3af86e75d068	16	FBgn0013686	106	60	2S17M458I113N37M4D33M1I14M1D7M3D81M1D21M1I65M1D397M1D22M2I33M2S	*	0	0	ACATTAATAGTATTCTTATAAAAAATATAATTATTTTGATATTTGGTCACTTTCGTACTAAAATATCACAATTTTTAAAGATAGAAACCAACCTGGCTTACACCGGTTTGAACTCAGATCATGTAAGAATTTAAAAAGTCGAACAGACTTAAAATTTTGAACGGCTACACCCAAAATTATATCAATCAACATCGAGGTCGCAATCTTTTTTATCGATATGAAGACTCTCCAAAAATTACGCTGTTATCCCTGAAAATGACACAATTTTTTAAAGCTTAAATTTATGAATATTTGATCCATTAATAATGATTAAAAAATTAAGTTACTTTAGGGATAACAGCGTAATTTTTGGAGAGTTCATATCGATAAAAAAGATTGCGACCTCGATGTTGGATTAAGATATAATTTTGGGTGTAGCCGTTCAAATTTTAAGTCTGTTCGGCAAATTCTTACATGATCTGAGTTCAAAACAAACCAAAAAGTCGAACAGACTTAAAATTTGAACAGCTACACCATTATAACTTAATCCAACATCGAGGTCGCAATCTTTTTTTATCGATATAAGTCTCAAAAATTACGCTGTTATCCCTAAAGTAACTTAATTTTTTAATCATTATTAATGGATCAAATATTCATAAATTTATGTTTTTAAAAATTAAAAGTTTTTTAAATTTTTAATATCACCCCAATAAAATATTTTTATTTATTAAAATTTAATTAATCTATATAATTAAAATAAAAAAAATATAAAGATTTATAGGGTCTTCTCGTCTTTTAAATAAATTTTAGCTTTTTGACTAAAAAATAAAATTCTATAAAAATTTTAAATGAAACAGTTAATATTTCGTCCAACCATTCATTCCAGCCTTCAATTAAAAGACTAATGATTATGCTACCTTTGCACTGTCAAAATACTGCGGCCATTTAAAATTTTCAGTGGGCAGGTTAGACTTTATATATAATTCAAAAAGACATGTTTTTGTTAAACAGGCGAATATTATTTTTGCCGAATTCTTTATTTAAACTTTTCATATAAATTAATTTTAACATTATTATATACTAATTTTATCATTATTGCTTAATTTTAATAATTAAAACTAACATTTTAATAAATAATTAAAATTTAATAAATAATTAATTTATAAAATAAATTATAACACACATTTTTTAATAATTGCTAATTCTAAGCATCC	:G>S:SJELGHSSSSIEIHHSJJSJCGASGPHSHLDCCH9KFBKFD=B.---2/<8IKSHHSKGM>FFLSFFSSCIKI8496>AEHI6E<CDCI?5444@B?KISSAHHLK@G<JSFKKGSMSSJ8:AABIKFCSALGS<H:SEAGJ@HIDSS:SGB88QGSQSSHJIOQHLISSEG>MEG430,,2969EFLJNRNISMKMDL@HPSNSBHF4F987677)(''''00/,+,-.3//8LNGSSKGSDSC==9976/....--.//>LD@D<9AC>9437?ALSSJGFSHMKSSHG<KSSDSI@@@@AHQES>AB2).B5C:HGHIGLK?>1H@LPBCAA@@ASGJHM=OO8MESS=JMJGFI<SFJECQGLEGD8311189BFOSSSJLIFSEHKGCHJGSHSKGKR<LNFCGSPFHINSR@D786620000029A??422/+))*?C=9ADEN@=BIMEESDFJC?A')++-..+*+0-.4=OF>HFKIFKE?BSCHKSHKJJFJKH6510,,,,.36@KEGSFAHC@BEKSEEAA1001FBIS:HIOSM<;;>13D@B?(&&&()*(((-5CC9@<<<<<LQFIGS+10K788:99899:;@:967968;HEGCBA?AAB@A<CSABCDDD?CBEGD@HCFGHFHEIG32789078;./210;?14/48<==:=@=>GGDDC@??>A?CDFCDECCAA1/.//2ACCR>D15;:;<;=B@@@@AEFDCCGFIAD?;ABA;5145AEGS>32223A@436:<>B.,,,-../C@E764@>;:;>=D?<BABECCF>99888>:D>=E?AABBBCCFB=<7556>31;DACCCC:AAACGHMIEB=<;4347?@@ACC?B>...3779BBCCGHNHGSH?:?CACDCDGF@<<<<=CCBDSFE=BBABCBKE<;:5449:;;??>>A=@JB@@E411002=:9888:79997=7>??=@??AASECF*)*,5>>@@BBEAD<4>GD5333334:;;@EDBBA>>C>?:::;;CCBAB@=>=?=;=>>EMG?MKSSRDGAKA@S6:HDDDFDEEHHHC97.-,4>ABIDDDBB>=</+*****,//248A@@>>>;<>=>>=BDCC<0/.3BKEEAFGJSD14BDC@=<?A=:776('))7099;==?>ADABBBJFE760//01<1/,/-/=BCBBBB===>B@>>65555/	NM:i:480	ms:i:659	AS:i:604	nn:i:0	ts:A:+	tp:A:P	cm:i:223	s1:i:732	s2:i:185	dv:f:0.0401