97592d3ab7dc59115a7f0c434776cbe823acf818 brianlee Wed Jan 22 11:54:21 2020 -0800 Updating the query.html examples to match the new RefSeq accessions on dev, not needing pushing out until the push of the new accessions refs #24808 diff --git src/hg/htdocs/goldenPath/help/query.html src/hg/htdocs/goldenPath/help/query.html index db399b4..342678f 100755 --- src/hg/htdocs/goldenPath/help/query.html +++ src/hg/htdocs/goldenPath/help/query.html @@ -48,38 +48,38 @@ query listed here will produce a result in every assembly. The list serves only to illustrate the different types of queries that can be performed. <table border="1"> <tr><th width="200">Query</th><th>Genome Browser Response</th></tr> <tr> <td>chr7</td> <td>Displays all of chromosome 7</td></tr> <tr> <td>chr3:1-1000000</td> <td>Displays the first million bases of chromosome 3, counting from the p-arm telomere</td></tr> <tr> <td>chr3:1000000+2000</td> <td>Displays a region of chromosome 3 that spans 2000 bases, starting with position 1000000</td> </tr> <tr> - <td>chrUn_gl000212</td> - <td>Displays all of the unplaced contig gl000212</td></tr> + <td>chrUn_GL000213v1</td> + <td>Displays all of the unplaced contig GL000213v1</td></tr> <tr> - <td>chr6_GL285171_random</td> - <td>Displays the unlocalized contig GL285171</td></tr> + <td>chr3_GL000221v1_random</td> + <td>Displays the unlocalized contig GL000221v1</td></tr> <tr> - <td>GL192360</td> - <td>Displays all of scaffold GL192360</td></tr> + <td>chr1_KN196472v1_fix</td> + <td>Displays all of patch fix KN196472v1</td></tr> <tr> <td>20p13</td> <td>Displays the region for band p13 on chromosome 20</td></tr> <tr> <tr> <td>GTATGTAGCCACGGAGCACCATTACCTGTCACCATTACCTGAATGGCTA</td> <td>Displays the first best match to this DNA sequence, e.g. chr21:33034835-33034883 for hg19</td> </tr> <tr> <td>374180</td> <td>Displays the region containing Entrez Gene identifier 374180</td></tr> <tr> <td>AA205474</td> <td>Displays the region containing the EST with GenBank accession AA205474 in the BRCA1 cancer gene on chromosome 17</td></tr> @@ -87,44 +87,44 @@ <td>AC008101</td> <td>Displays the region containing the clone with GenBank accession AC008101</td></tr> <tr> <td>AF083811</td> <td>Displays the region containing the mRNA with GenBank accession number AF083811</td></tr> <tr> <td>NM_017414</td> <td>Displays the region containing RefSeq identifier NM_017414</td></tr> <tr> <td>NP_059110</td> <td>Displays the region containing protein accession number NP_059110</td></tr> <tr> <td>PRNP</td> <td>Displays the region containing HUGO Gene Nomenclature Committee identifier PRNP</td></tr> <tr> - <td nowrap>RH18061;RH80175<br>15q11;15q13<br>rs1042522;rs1800370</td> + <td nowrap>RH18061;RH80175<br>15q11;15q13<br>NM_012090.5;NM_012421.4</td> <td nowrap>Displays the region between genome landmarks, such as the STS markers RH18061 and - RH80175, or chromosome<br> bands 15q11 to 15q13, or SNPs rs1042522 and rs1800370. This syntax + RH80175, or chromosome<br> bands 15q11 to 15q13, or SNPs NM_000310.4 and NM_012090.5. This syntax may also be used for other range queries,<br>such as between uniquely determined ESTs, mRNAs, - refSeqs, etc.</td></tr> + refSeqs, SNPS, etc.</td></tr> <tr id="HGVS"> - <td nowrap>NM_000310.3(PPT1):c.271_287del17insTT<br> NM_007262.4(PARK7):c.-24+75_-24+92dup<br> + <td nowrap>NM_000310.3(PPT1):c.271_287del17insTT<br> NM_007262.5(PARK7):c.-24+75_-24+92dup<br> NM_006172.3(NPPA):c.456_*1delAA<br> MYH11:c.503-14_503-12del<br> - NM_198576.3(AGRN):c.1057C>T<br> NM_198056.2:c.1654G>T<br> NP_002993.1:p.Asp92Glu<br> + NM_198576.4(AGRN):c.1057C>T<br> NM_198056.2:c.1654G>T<br> NP_002993.1:p.Asp92Glu<br> NP_002993.1:p.D92E<br> BRCA1 Ala744Cys<br> BRCA1 A744C<br> LRG_100t1:c.4G>A<br> LRG_100t1:n.1<br> LRG_456p1:p.Ser190Leu<br>LRG_321:g.16409_16461del<br>ENST00000002596.5:c.-108-6848A>G<br> ENSP00000005178.5:p.Val20Gly<br> - chrX:g.31500000_31600000del<br> NR_111987:n.-1 <br> NM_015102.4:n.3086-2<br> - NM_033517:c.1307_1309del</td> + chrX:g.31500000_31600000del<br> NR_111987:n.-1 <br> NM_015102.5:n.3038-2<br> + NM_001372044:c.1528_1530del</td> <td>Displays the region containing <a href="http://varnomen.hgvs.org/" target="_blank">HGVS</a> term</td></tr> <!-- commented out -- not working <tr> <td>15q11;15q13</td> <td>bands 15q11 to 15q13, or SNPs rs1042522 and rs1800370. This syntax may also be used for other range queries</td></tr> <tr> <td>rs1042522;rs1800370</td> <td>such as between uniquely determined ESTs, mRNAs, refSeqs, etc.</td></tr> --> <tr> <td>chr1 0 1000</td> <td>When entered without ":" and "-", uses 0-based, half-open coordinates (like custom tracks and internal table coordinates), so displays chr1:1-1000</td> </tr>