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Database: saiBol1 Primary Table: xenoRefSeqAli Row Count: 593,440 Data last updated: 2020-08-20
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
| field | example | SQL type | description |
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| bin | 585 | smallint(5) unsigned | Indexing field to speed chromosome range queries. |
| matches | 1984 | int(10) unsigned | Number of bases that match that aren't repeats |
| misMatches | 297 | 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 | 27 | int(10) unsigned | Number of inserts in query |
| qBaseInsert | 1936 | int(10) unsigned | Number of bases inserted in query |
| tNumInsert | 29 | int(10) unsigned | Number of inserts in target |
| tBaseInsert | 1354 | int(10) unsigned | Number of bases inserted in target |
| strand | ++ | char(2) | + or - for strand. First character query, second target (optional) |
| qName | NM_001082756 | varchar(255) | Query sequence name |
| qSize | 4471 | int(10) unsigned | Query sequence size |
| qStart | 22 | int(10) unsigned | Alignment start position in query |
| qEnd | 4239 | int(10) unsigned | Alignment end position in query |
| tName | AGCE01148336 | varchar(255) | Target sequence name |
| tSize | 38010 | int(10) unsigned | Target sequence size |
| tStart | 8739 | int(10) unsigned | Alignment start position in target |
| tEnd | 12374 | int(10) unsigned | Alignment end position in target |
| blockCount | 37 | int(10) unsigned | Number of blocks in alignment |
| blockSizes | 204,29,36,211,178,220,150,5... | longblob | Size of each block |
| qStarts | 22,226,304,349,560,739,962,... | longblob | Start of each block in query. |
| tStarts | 8739,8973,9051,9087,9299,94... | longblob | Start of each block in target. |
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Connected Tables and Joining Fields
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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)
saiBol1.all_mrna.qName (via xenoRefSeqAli.qName)
saiBol1.xenoMrna.qName (via xenoRefSeqAli.qName)
saiBol1.xenoRefFlat.name (via xenoRefSeqAli.qName)
saiBol1.xenoRefGene.name (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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| 585 | 1984 | 297 | 0 | 0 | 27 | 1936 | 29 | 1354 | ++ | NM_001082756 | 4471 | 22 | 4239 | AGCE01148336 | 38010 | 8739 | 12374 | 37 | 204,29,36,211,178,220,150,53,45,31,118,81,19,39,15,27,17,7,14,60,12,7,10,5,39,11,7,14,18,24,75,42,101,95,156,60,51, | 22,226,304,349,560,739,962,1995,2055,2127,2166,2284,2365,2429,2476,2491,2518,2549,2556,2575,2685,2698,2755,2765,2987,3034,3050,3 ... | 8739,8973,9051,9087,9299,9477,9697,9847,9906,9967,10001,10120,10204,10268,10312,10328,10357,10374,10397,10415,10526,10538,10605, ... |
| 585 | 3681 | 402 | 0 | 0 | 33 | 1611 | 34 | 745 | ++ | NM_002577 | 6139 | 271 | 5965 | AGCE01148336 | 38010 | 8739 | 13567 | 50 | 204,29,42,216,176,222,150,152,232,135,112,39,6,8,23,5,9,5,60,51,24,38,59,84,53,46,84,456,124,37,54,150,81,100,15,24,15,7,62,96,4 ... | 271,475,542,593,809,986,1211,2249,2410,2644,2788,2900,2940,2947,2956,2980,2986,2995,3004,3066,3188,3283,3323,3436,3520,3574,3620 ... | 8739,8973,9040,9082,9299,9475,9697,9847,10001,10233,10380,10493,10532,10538,10552,10584,10589,10601,10606,10667,10793,10867,1090 ... |
| 585 | 2376 | 281 | 0 | 0 | 44 | 2721 | 40 | 2172 | ++ | NM_001206727 | 5644 | 11 | 5389 | AGCE01148336 | 38010 | 8739 | 13568 | 52 | 204,14,31,214,178,222,150,52,51,13,31,13,33,67,11,30,24,54,33,7,40,39,17,12,100,58,9,24,47,125,95,127,43,38,33,15,72,36,12,6,9,6 ... | 11,215,293,333,547,726,951,1971,2029,2088,2108,2198,2233,2321,2395,2599,2650,2921,2980,3015,3029,3182,3267,3445,3468,3642,3729,3 ... | 8739,8973,9051,9082,9297,9475,9697,9847,9899,9954,9967,10050,10089,10173,10244,10499,10552,10821,10876,10909,10922,11064,11152,1 ... |
| 585 | 3737 | 420 | 0 | 0 | 30 | 1478 | 27 | 662 | ++ | NR_027053 | 8226 | 2572 | 8207 | AGCE01148336 | 38010 | 8749 | 13568 | 40 | 194,29,42,106,101,176,74,148,150,152,232,141,154,14,21,7,75,51,24,39,39,57,21,42,53,131,204,376,96,149,205,87,62,96,48,107,66,62 ... | 2572,2766,2833,2884,2990,3091,3268,3343,3494,4532,4693,4927,5069,5224,5239,5263,5271,5348,5470,5514,5557,5598,5709,5746,5788,584 ... | 8749,8973,9040,9082,9197,9299,9475,9549,9697,9847,10001,10233,10378,10532,10552,10584,10591,10667,10793,10823,10867,10906,11019, ... |
| 585 | 1241 | 181 | 0 | 0 | 19 | 3748 | 17 | 3057 | ++ | NM_177326 | 5741 | 250 | 5420 | AGCE01148336 | 38010 | 8764 | 13243 | 23 | 179,11,31,218,179,211,152,22,88,12,15,8,24,30,5,11,9,19,51,33,66,15,33, | 250,429,507,547,765,951,1165,2409,2435,2566,2684,2721,2734,2814,2865,2870,2882,2901,3155,3917,4059,4129,5387, | 8764,8973,9051,9082,9301,9486,9697,10067,10098,10186,10346,10403,10415,10512,10571,10578,10589,10610,10861,11702,11845,11911,132 ... |
| 585 | 2537 | 250 | 0 | 0 | 22 | 1182 | 17 | 324 | ++ | NM_001265935 | 4037 | 57 | 4026 | AGCE01148336 | 38010 | 8768 | 11879 | 28 | 173,42,216,176,222,152,36,113,232,99,36,118,54,23,5,75,23,18,11,19,7,39,59,88,30,11,102,608, | 57,299,350,566,743,968,2009,2045,2167,2401,2501,2542,2660,2714,2738,2744,2830,2936,2973,2987,3006,3015,3056,3173,3263,3294,3306, ... | 8768,9040,9082,9299,9475,9697,9849,9886,10001,10233,10332,10374,10493,10552,10584,10589,10674,10799,10822,10833,10855,10866,1090 ... |
| 624 | 841 | 97 | 0 | 0 | 13 | 201 | 9 | 13936 | +- | NR_157816 | 1160 | 0 | 1139 | JH378175 | 11673789 | 5176848 | 5191722 | 15 | 87,132,58,66,36,21,38,19,72,46,24,54,81,86,118, | 0,143,275,342,412,451,490,529,549,636,687,727,783,926,1021, | 6482067,6494156,6495905,6495970,6496038,6496076,6496330,6496368,6496387,6496464,6496510,6496544,6496598,6496737,6496823, |
| 585 | 291 | 120 | 0 | 0 | 2 | 102 | 1 | 74 | ++ | NM_001089700 | 2044 | 693 | 1206 | AGCE01148336 | 38010 | 9364 | 9849 | 3 | 33,228,150, | 693,825,1056, | 9364,9471,9699, |
| 639 | 3269 | 144 | 0 | 27 | 11 | 604 | 23 | 99001 | ++ | NM_001382223 | 4061 | 15 | 4059 | JH378107 | 58292249 | 7097881 | 7200322 | 29 | 69,83,291,201,74,161,177,139,147,108,92,140,92,78,61,121,95,157,117,271,75,150,167,24,80,25,139,83,23, | 15,86,170,461,662,736,1036,1213,1352,1499,1607,1699,1839,1931,2009,2206,2327,2422,2743,2860,3132,3244,3468,3675,3708,3788,3813,3 ... | 7097881,7097950,7098033,7132890,7134009,7136257,7151382,7152052,7154953,7158236,7160019,7161980,7167869,7169684,7172271,7176351, ... |
| 598 | 592 | 224 | 0 | 0 | 0 | 0 | 5 | 13765 | +- | NM_001255490 | 1668 | 325 | 1141 | JH378252 | 4400728 | 1766367 | 1780948 | 6 | 123,234,100,72,152,135, | 325,448,682,782,854,1006, | 2619780,2621386,2623778,2625656,2629562,2634226, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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US Server