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Database: choHof1 Primary Table: xenoRefSeqAli Row Count: 889,220   Data last updated: 2020-08-18
Format description: Summary info about a patSpace alignment On download server: MariaDB table dump directory
field | example | SQL type | description |
bin | 73 | smallint(5) unsigned | Indexing field to speed chromosome range queries. |
matches | 2831 | int(10) unsigned | Number of bases that match that aren't repeats |
misMatches | 366 | int(10) unsigned | Number of bases that don't match |
repMatches | 0 | int(10) unsigned | Number of bases that match but are part of repeats |
nCount | 0 | int(10) unsigned | Number of 'N' bases |
qNumInsert | 22 | int(10) unsigned | Number of inserts in query |
qBaseInsert | 824 | int(10) unsigned | Number of bases inserted in query |
tNumInsert | 20 | int(10) unsigned | Number of inserts in target |
tBaseInsert | 149556 | int(10) unsigned | Number of bases inserted in target |
strand | +- | char(2) | + or - for strand. First character query, second target (optional) |
qName | NM_001106465 | varchar(255) | Query sequence name |
qSize | 5085 | int(10) unsigned | Query sequence size |
qStart | 1064 | int(10) unsigned | Alignment start position in query |
qEnd | 5085 | int(10) unsigned | Alignment end position in query |
tName | scaffold_0 | varchar(255) | Target sequence name |
tSize | 197267 | int(10) unsigned | Target sequence size |
tStart | 37271 | int(10) unsigned | Alignment start position in target |
tEnd | 190024 | int(10) unsigned | Alignment end position in target |
blockCount | 32 | int(10) unsigned | Number of blocks in alignment |
blockSizes | 642,173,26,141,172,39,39,11... | longblob | Size of each block |
qStarts | 1064,1706,1879,2072,2213,24... | longblob | Start of each block in query. |
tStarts | 7243,72331,84322,111462,157... | longblob | Start of each block in target. |
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Connected Tables and Joining Fields
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choHof1.all_mrna.qName (via xenoRefSeqAli.qName)
choHof1.xenoMrna.qName (via xenoRefSeqAli.qName)
choHof1.xenoRefFlat.name (via xenoRefSeqAli.qName)
choHof1.xenoRefGene.name (via xenoRefSeqAli.qName)
hgFixed.gbCdnaInfo.acc (via xenoRefSeqAli.qName)
hgFixed.gbMiscDiff.acc (via xenoRefSeqAli.qName)
hgFixed.gbSeq.acc (via xenoRefSeqAli.qName)
hgFixed.gbWarn.acc (via xenoRefSeqAli.qName)
hgFixed.imageClone.acc (via xenoRefSeqAli.qName)
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Sample Rows
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bin | matches | misMatches | repMatches | nCount | qNumInsert | qBaseInsert | tNumInsert | tBaseInsert | strand | qName | qSize | qStart | qEnd | tName | tSize | tStart | tEnd | blockCount | blockSizes | qStarts | tStarts |
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73 | 2831 | 366 | 0 | 0 | 22 | 824 | 20 | 149556 | +- | NM_001106465 | 5085 | 1064 | 5085 | scaffold_0 | 197267 | 37271 | 190024 | 32 | 642,173,26,141,172,39,39,111,10,12,7,14,86,53,77,80,9,150,58,29,60,81,97,30,22,15,64,123,160,206,93,318, | 1064,1706,1879,2072,2213,2476,2539,2609,2727,2737,2749,2763,2778,2865,2929,3009,3089,3133,3287,3349,3378,3440,3556,3655,3702,373 ... | 7243,72331,84322,111462,157184,157453,157524,157585,157701,157712,157726,157733,157747,157833,157886,157963,158045,158088,158238 ... |
73 | 2945 | 353 | 0 | 0 | 25 | 541 | 22 | 149455 | +- | NM_001163348 | 5179 | 1340 | 5179 | scaffold_0 | 197267 | 37271 | 190024 | 34 | 642,173,26,139,172,75,39,54,130,56,74,33,46,36,145,58,30,40,155,76,30,22,15,64,123,155,24,29,36,15,175,93,78,240, | 1340,1982,2155,2182,2321,2561,2646,2777,2832,2963,3028,3105,3138,3184,3228,3385,3447,3477,3519,3676,3754,3801,3829,3845,3910,403 ... | 7243,72331,84322,111464,157184,157431,157524,157649,157703,157833,157889,157963,157997,158045,158088,158238,158296,158328,158368 ... |
73 | 2815 | 349 | 0 | 0 | 24 | 540 | 22 | 149589 | +- | NM_001163349 | 5044 | 1340 | 5044 | scaffold_0 | 197267 | 37271 | 190024 | 34 | 642,173,26,3,174,75,39,54,130,56,74,33,46,36,145,58,30,40,155,76,30,22,15,64,123,155,24,29,36,15,175,93,78,240, | 1340,1982,2155,2181,2184,2426,2511,2642,2697,2828,2893,2970,3003,3049,3093,3250,3312,3342,3384,3541,3619,3666,3694,3710,3775,389 ... | 7243,72331,84322,84378,157182,157431,157524,157649,157703,157833,157889,157963,157997,158045,158088,158238,158296,158328,158368, ... |
73 | 2937 | 351 | 0 | 0 | 25 | 542 | 23 | 149465 | +- | NM_001163350 | 5170 | 1340 | 5170 | scaffold_0 | 197267 | 37271 | 190024 | 35 | 642,173,27,64,60,176,75,39,54,130,56,74,33,46,36,145,58,30,40,155,76,30,22,15,64,123,155,24,29,36,15,175,93,78,240, | 1340,1982,2155,2184,2248,2308,2552,2637,2768,2823,2954,3019,3096,3129,3175,3219,3376,3438,3468,3510,3667,3745,3792,3820,3836,390 ... | 7243,72331,84322,95036,97281,157180,157431,157524,157649,157703,157833,157889,157963,157997,158045,158088,158238,158296,158328,1 ... |
73 | 2947 | 353 | 0 | 0 | 25 | 707 | 22 | 149453 | +- | NM_030699 | 5347 | 1340 | 5347 | scaffold_0 | 197267 | 37271 | 190024 | 34 | 642,173,26,141,172,75,39,54,130,56,74,33,46,36,145,58,30,40,155,76,30,22,15,64,123,155,24,29,36,15,175,93,78,240, | 1340,1982,2155,2348,2489,2729,2814,2945,3000,3131,3196,3273,3306,3352,3396,3553,3615,3645,3687,3844,3922,3969,3997,4013,4078,420 ... | 7243,72331,84322,111462,157184,157431,157524,157649,157703,157833,157889,157963,157997,158045,158088,158238,158296,158328,158368 ... |
73 | 2878 | 350 | 0 | 0 | 25 | 542 | 22 | 149525 | +- | NM_133488 | 5110 | 1340 | 5110 | scaffold_0 | 197267 | 37271 | 190024 | 34 | 642,173,27,64,176,75,39,54,130,56,74,33,46,36,145,58,30,40,155,76,30,22,15,64,123,155,24,29,36,15,175,93,78,240, | 1340,1982,2155,2184,2248,2492,2577,2708,2763,2894,2959,3036,3069,3115,3159,3316,3378,3408,3450,3607,3685,3732,3760,3776,3841,396 ... | 7243,72331,84322,95036,157180,157431,157524,157649,157703,157833,157889,157963,157997,158045,158088,158238,158296,158328,158368, ... |
73 | 1851 | 189 | 0 | 0 | 12 | 118 | 13 | 149145 | +- | NM_001080369 | 3018 | 837 | 2995 | scaffold_0 | 197267 | 38839 | 190024 | 18 | 642,173,27,66,178,16,87,24,40,94,170,25,91,51,16,206,36,98, | 837,1479,1652,1679,1745,1940,2007,2095,2129,2172,2286,2457,2487,2578,2633,2650,2860,2897, | 7243,72331,84322,95034,157180,157384,157447,157539,157574,157616,157728,157898,157927,158019,158072,158088,158294,158330, |
585 | 242 | 103 | 0 | 0 | 1 | 9 | 1 | 12 | +- | NM_001312817 | 1133 | 218 | 572 | scaffold_153089 | 4438 | 1699 | 2056 | 2 | 165,180, | 218,392, | 2382,2559, |
585 | 139 | 44 | 0 | 0 | 0 | 0 | 0 | 0 | ++ | NM_001312775 | 982 | 130 | 313 | scaffold_153170 | 5960 | 5350 | 5533 | 1 | 183, | 130, | 5350, |
585 | 235 | 92 | 0 | 0 | 1 | 75 | 1 | 81 | +- | NM_001312791 | 500 | 41 | 443 | scaffold_149000 | 4729 | 1523 | 1931 | 2 | 261,66, | 41,377, | 2798,3140, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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