Bioinformatics Recipe Cookbook

Run Parameters
Parameters used during the run:
  • Accession number for the first sequence: AF086833
  • Accession number for the second sequence: KR105294
Output Messages
Messages printed to the standard output stream:
*** The alignment as a CIGAR string:
cg:Z:9626M1D9268M
*** The alignment as an MD tag:
MD:Z:65C21C5A26A4A42C5T20A3C1G31A60C3G8T7T0T2G3T2A3T16T14G9A56A8G118A35A65G78C49A1A42A23T174C13C32G56C0T109T107A29A8T38A11T35A8C95T56G137G5T12A16G22A51T14T26G22T23G5T6T3C9A15C8G26T35A5T59G17G20C50T23C2G19C18G18T7C53T56C17A47T8A18T25G2G10A46G2C12C2C20G13A61T70G27T12T0C2A1T74T2T72C35T42C75A10G80C288C80C36A151C11C41T110A23G81C0C17G1A36C35G21G23T12A3T21T18C28G28G119T24A47G32C59T134C32A41T56G56C41A188A53T135A40T30A4G9C1T4G4C4T40T20A24T10G21A17T34T22T4C19G18T22A8A10A10G13C15C77T16G16C1T0G12A2C18G3A13C95A8C11C89A31C0A191G23T167T8C41C102A10A8T123T13G48G14C67G19A29C3T1C1T10C69A12C3A32T1T21C0C24C6A6T8C9A5T9C10C92C26A13C30T45C34G10T18T26A14G14T29A2C32T3T16C15C169C52T13C4T2A3G4G17C16G2T32T17T72T3C5G54A39G3C2G5G35G10G8C13T11C31G8T33A236T8G2G140A57A16A8A8G53A23G143T251G9A7G5G6C8G13C5T4G3T29T59T28C4^A14C4C53A9C12G1T7G55A6G14T37A61G12G7A0T5G19T4C30A7T15C43G31A33T0T15C9G19G2A28T36T42T89C11G8G104T2C5T26A21T35C1G200C5G109T63A23G11T26G1A15A30T14T137C41G17C8T6T18G13C0A16G3C16T10T17A13C60A52T38A20A56C8G5C23G45G16G11A44C30T49A11G59T53A72A43C9G61C69A7T8T89T8C20C11A14T53A17G26A74T92A17C17T5C41T8G11G59A26C62C47A23T5T65A35C44C113G53T5A62A125A17G6G10C119A35T29C4A21A140T83C50G23T29T5G2C158C125C44C5C47G32A5A29T2G8C45C55A23A20C86T20T14A51T43A8A23G32G2C71A182A14C53T59G2T95A44A14T50C16G39C5T14T4G21T38C35C5A65G107T74G17T104A50G0C13C11G8T3T40A22G69A23A21T5G5G44G51A9A41A29C20T11T18C21T15G35C77C59A61G3C17A62T193A9G23A39T20A7T44T27T22T29T2A80A38A41T2G11T56C30A25A17A2T113G80C14C104G17T8T14C0C9C13T45A7A2C8C9A16C2T6T9A37G23C7A1T20T27A29A18C2T14T15A16T29A5A13T8C48C29T3A25G2G74A26G1C23T61
*** The alignment as a CS tag:
cs:Z::65*ct:21*ct:5*ac:26*ag:4*ag:42*ct:5*tc:20*ag:3*ct:1*ga:31*ac:60*ct:3*ga:8*tc:7*tc*tc:2*ga:3*tc:2*ag:3*tc:16*tc:14*ga:9*at:56*ag:8*ga:118*ag:35*at:65*ga:78*ct:49*ag:1*ag:42*ag:23*tc:174*ct:13*ct:32*ga:56*ct*tc:109*tc:107*ag:29*ac:8*tc:38*ag:11*ta:35*ag:8*ct:95*tg:56*ga:137*ga:5*tc:12*ag:16*ga:22*ag:51*tc:14*tc:26*ga:22*tc:23*gc:5*tc:6*tc:3*ca:9*ag:15*ct:8*gt:26*tc:35*ac:5*tc:59*ga:17*ga:20*ct:50*tc:23*ct:2*ga:19*ct:18*ga:18*tc:7*ct:53*tc:56*ct:17*ag:47*tc:8*at:18*tc:25*ga:2*ga:10*ag:46*gt:2*ct:12*ct:2*ct:20*ga:13*ac:61*tg:70*ga:27*tg:12*tc*ct:2*ag:1*tc:74*tc:2*tc:72*ca:35*tc:42*ct:75*ag:10*ga:80*ct:288*ct:80*ct:36*ag:151*ct:11*ct:41*tc:110*ag:23*ga:81*ct*ct:17*ga:1*ac:36*ct:35*ga:21*ga:23*tc:12*at:3*tg:21*tc:18*ct:28*ga:28*ga:119*tc:24*ag:47*ga:32*ct:59*tc:134*ct:32*ag:41*tc:56*ga:56*ct:41*at:188*at:53*tc:135*ag:40*tc:30*at:4*ga:9*ct:1*tc:4*ga:4*ct:4*tc:40*tc:20*ag:24*tc:10*ga:21*ag:17*tc:34*tc:22*tc:4*ct:19*ga:18*tc:22*ag:8*ag:10*ag:10*ga:13*ct:15*ct:77*tc:16*ga:16*ct:1*tg*ga:12*ag:2*ct:18*ga:3*ag:13*ct:95*ag:8*ct:11*ct:89*ag:31*ct*ag:191*ga:23*tc:167*tg:8*ct:41*ct:102*ag:10*ag:8*tc:123*tc:13*gc:48*ga:14*ca:67*ga:19*ag:29*ct:3*tc:1*ct:1*tc:10*ca:69*ag:12*ct:3*ag:32*tc:1*tc:21*ct*ct:24*ct:6*ag:6*tc:8*ct:9*ag:5*tc:9*ct:10*ct:92*ca:26*ag:13*ct:30*tc:45*ct:34*ga:10*tc:18*tc:26*ag:14*ga:14*tc:29*ag:2*ca:32*tc:3*tc:16*ct:15*ct:169*ct:52*tc:13*ct:4*tc:2*ac:3*ga:4*ga:17*ct:16*ga:2*tc:32*tc:17*tc:72*tc:3*ca:5*ga:54*ag:39*ga:3*ca:2*ga:5*ga:35*ga:10*ga:8*ct:13*tc:11*ca:31*gc:8*tc:33*ac:236*tc:8*ga:2*ga:140*ac:57*ac:16*ac:8*ag:8*ga:53*ag:23*ga:143*tc:251*ga:9*ag:7*ga:5*ga:6*ct:8*ga:13*ct:5*ta:4*gt:3*tc:29*tc:59*tg:28*ct:4-a:14*ct:4*ct:53*ac:9*ct:12*gc:1*ta:7*gc:55*ag:6*gt:14*ta:37*ag:61*ga:12*ga:7*ag*tc:5*ga:19*tc:4*ct:30*ag:7*tg:15*ct:43*ga:31*at:33*tc*tc:15*ct:9*ga:19*ga:2*ag:28*ta:36*tc:42*tc:89*ct:11*ga:8*ga:104*tc:2*ca:5*tc:26*at:21*tc:35*ct:1*ga:200*ct:5*ga:109*ta:63*ag:23*ga:11*tc:26*ga:1*ag:15*ag:30*ta:14*tc:137*ct:41*gt:17*ct:8*ta:6*tg:18*ga:13*ct*ag:16*ga:3*ca:16*tc:10*tc:17*ag:13*ct:60*ac:52*tc:38*at:20*ag:56*ca:8*ga:5*ct:23*ga:45*ga:16*ga:11*ag:44*ct:30*tc:49*ac:11*ga:59*tc:53*ag:72*ac:43*ct:9*ga:61*ct:69*ag:7*tc:8*tc:89*tc:8*ct:20*ct:11*ag:14*tc:53*ag:17*ga:26*ac:74*ta:92*ac:17*ct:17*tc:5*ca:41*tc:8*ga:11*ga:59*ag:26*ct:62*ct:47*ag:23*tc:5*tc:65*ag:35*ct:44*ct:113*ga:53*tc:5*ag:62*ag:125*ag:17*ga:6*ga:10*ct:119*ag:35*tc:29*ct:4*ag:21*ag:140*tc:83*ct:50*ga:23*tc:29*tc:5*ga:2*ct:158*ct:125*ct:44*ct:5*ct:47*ga:32*ag:5*ac:29*tc:2*ga:8*ca:45*ct:55*ag:23*ag:20*ct:86*tc:20*ta:14*ag:51*tg:43*ac:8*at:23*ga:32*ga:2*ct:71*ag:182*ag:14*ct:53*tc:59*ga:2*tg:95*ag:44*ag:14*tc:50*ct:16*ga:39*ct:5*tc:14*tc:4*ga:21*tc:38*ct:35*ct:5*ag:65*ga:107*tc:74*ga:17*tc:104*ag:50*ga*ct:13*ct:11*gt:8*tc:3*tc:40*ac:22*ga:69*ag:23*ag:21*tg:5*ga:5*ga:44*ga:51*ag:9*ag:41*ag:29*ca:20*tc:11*tc:18*ca:21*tc:15*ga:35*ct:77*ct:59*ag:61*ga:3*ct:17*ag:62*tc:193*ag:9*ga:23*ag:39*tc:20*ag:7*tc:44*tc:27*tc:22*tg:29*tc:2*ag:80*ag:38*ag:41*tc:2*gt:11*tc:56*ct:30*ag:25*ag:17*ag:2*tc:113*ga:80*ct:14*ct:104*ga:17*tc:8*ta:14*ct*ct:9*ct:13*tc:45*ac:7*ag:2*ct:8*ct:9*ag:16*ct:2*tc:6*tc:9*ag:37*ga:23*ct:7*ag:1*tc:20*tc:27*at:29*ag:18*ct:2*tc:14*tc:15*ag:16*tc:29*ag:5*ag:13*ta:8*ct:48*ct:29*tc:3*at:25*ga:2*gt:74*ag:26*ga:1*ct:23*tc:61
Other Messages
Messages printed to the standard error stream:
[M::mm_idx_gen::0.001*0.00] collected minimizers
[M::mm_idx_gen::0.002*0.00] sorted minimizers
[M::main::0.002*0.00] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.002*0.00] mid_occ = 3
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.002*0.00] distinct minimizers: 3590 (99.94% are singletons); average occurrences: 1.001; average spacing: 5.278
[M::worker_pipeline::0.006*0.72] mapped 1 sequences
[M::main] Version: 2.12-r827
[M::main] CMD: minimap2 -c --MD 1.fa 2.fa
[M::main] Real time: 0.006 sec; CPU: 0.004 sec
[M::mm_idx_gen::0.001*0.00] collected minimizers
[M::mm_idx_gen::0.002*0.00] sorted minimizers
[M::main::0.002*0.00] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.002*0.00] mid_occ = 3
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.002*0.00] distinct minimizers: 3590 (99.94% are singletons); average occurrences: 1.001; average spacing: 5.278
[M::worker_pipeline::0.005*0.73] mapped 1 sequences
[M::main] Version: 2.12-r827
[M::main] CMD: minimap2 --cs 1.fa 2.fa
[M::main] Real time: 0.006 sec; CPU: 0.004 sec

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