Hi,
When aligning a sequence to an augmented reference database I got a different ms, I wonder does ms depend on tp?
One reference seq:
minimap2 -cx map-ont one.fa query.fa [M::mm_idx_gen::0.001*5.95] collected minimizers [M::mm_idx_gen::0.002*4.99] sorted minimizers [M::main::0.002*4.98] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.002*4.79] mid_occ = 10 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.002*4.63] distinct minimizers: 1848 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.411; total length: 10000 SRR23690005.810506 4901 0 4887 + NZ_CP060632.1_2416720-2426719:- 10000 1879 6750 4751 4890 60 NM:i:139 ms:i:8942 AS:i:8934 nn:i:0 tp:A:P cm:i:676 s1:i:4011 s2:i:0 de:f:0.0268 rl:i:0 cg:Z:68M2I31M1I1203M1I1788M1D266M4I33M3I208M1D81M1I311M1I323M1I134M2I233M1D1M2I4M1I184M
Two reference seqs:
minimap2 -cx map-ont two.fa query.fa [M::mm_idx_gen::0.004*3.47] collected minimizers [M::mm_idx_gen::0.005*3.31] sorted minimizers [M::main::0.005*3.31] loaded/built the index for 2 target sequence(s) [M::mm_mapopt_update::0.005*3.22] mid_occ = 10 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 2 [M::mm_idx_stat::0.006*3.15] distinct minimizers: 2397 (45.06% are singletons); average occurrences: 1.549; average spacing: 5.385; total length: 20000 SRR23690005.810506 4901 0 4887 + CABOHD010000001.1_23218-33217:- 10000 257 5129 4847 4891 60 NM:i:44 ms:i:7856 AS:i:9504 nn:i:0 tp:A:P cm:i:842 s1:i:4700 s2:i:4011 de:f:0.0074 rl:i:0 cg:Z:67M1I4M1D2M2I1229M1I1788M1D266M4I33M3I208M1D81M1I311M1I323M1I134M2I233M1D1M2I4M1I184M SRR23690005.810506 4901 0 4887 + NZ_CP060632.1_2416720-2426719:- 10000 1879 6750 4751 4890 0 NM:i:139 ms:i:2916 AS:i:8934 nn:i:0 tp:A:S cm:i:676 s1:i:4011 de:f:0.0268 rl:i:0 cg:Z:68M2I31M1I1203M1I1788M1D266M4I33M3I208M1D81M1I311M1I323M1I134M2I233M1D1M2I4M1I184M
AS, de and cg are all identical.
Here are the sequences:
example.zip
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