db75ac2f74d3149efdb945d1efe966b27ec0def8 jnavarr5 Thu Apr 30 15:39:17 2026 -0700 Adding a note about Pieter de Jong's contribution to the BAC tracks, refs #35059 diff --git src/hg/makeDb/trackDb/human/cloneEndSuper.html src/hg/makeDb/trackDb/human/cloneEndSuper.html index ab0dcca46d8..d6748396a6b 100644 --- src/hg/makeDb/trackDb/human/cloneEndSuper.html +++ src/hg/makeDb/trackDb/human/cloneEndSuper.html @@ -1,107 +1,117 @@ <H2>Description</H2> <P> This track shows the NCBI clone end mappings from the <A HREF="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" TARGET=_blank>NCBI Clone DB</A> database. Libraries with more than 30,000 clones are included in this track display. While the NCBI Clone DB database interface has been retired and is no longer available, they were archived and are still accessible for download at NCBI and through the UCSC Genome Browser.</P> <P> <b>Clone availability:</b> most of the clone libraries shown here can no longer be ordered. Two librarires that we show are exceptions and are still available for ordering from <A HREF="https://bacpacresources.org/libraries.php" TARGET=_blank>BACPAC Genomics</A> who still sells the libraries made by and formerly distributed by Children's Hospital Oakland Research Institute (CHORI): the <A HREF="hgTrackUi?g=bacRearray32k">BCGSC Human 32k BAC Re-Array</A> (minimal tiling set, mostly RP11 and CTD clones) and the CHORI-17 (CH17) BAC library from a hydatidiform mole.</P> <P> Bacterial artificial chromosomes (BACs) are a key part of many large-scale sequencing projects. A BAC typically consists of 50 - 300 kb of DNA. During the early phase of a sequencing project, it is common to sequence a single read (approximately 500 bases) off each end of a large number of BACs. Later on in the project, these BAC end reads can be mapped to the genome sequence.</P> <P> These BAC end pairs can be useful for validating the assembly over relatively long ranges. In some cases, the BACs are useful biological reagents. This track can also be used for determining which BAC contains a given gene, useful information for certain wet lab experiments.</P> <P> The scoring scheme used for this annotation assigns 1000 to an alignment when the BAC end pair aligns to only one location in the genome (after filtering). When a BAC end pair or clone aligns to multiple locations, the score is calculated as 1500/(number of alignments).</P> <h2>Display Conventions and Configuration</h2> <p> Items in this track are colored according to their strand orientation. Blue indicates alignment to the forward strand, and green indicates alignment to the negative strand. </p> <H2>Methods</H2> <P> The mappings of these BAC end sequences are taken directly from the NCBI Clone DB FTP site <A HREF="ftp://ftp.ncbi.nih.gov/repository/clone/reports/Homo_sapiens/" TARGET=_blank>ftp.ncbi.nih.gov/repository/clone/reports/Homo_sapiens/</A> *.GCF_000001405.26.106.*.gff files.</P> <P> UCSC filtered the NCBI Clone DB mapped ends to drop ends that mapped to a region that was three times longer than the median size of the clones in the library. Only libraries with more than 30,000 clones are included in this track display.</P> <P> Click through on displayed items to the Clone DB database information, including <A HREF="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" TARGET=_blank>Clone DB distributor</A> references.</P> <TABLE BORDER=1> <TR><TH COLSPAN=7>clone information from NCBI Clone DB and UCSC mapping statistics</TH></TR> <TR><TH>library<BR>name</TH> <TH>total<BR>clones</TH> <TH>total end<BR>sequences</TH> <TH>NCBI mapped<BR>ends</TH> <TH>UCSC filtered<BR>ends</TH> <TH>UCSC<BR>dropped</TH> <TH>per-cent<BR>dropped</TH> </TR> <TR><TH ALIGN=LEFT><A HREF="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" TARGET="_blank">ABC8</A></TH><TD ALIGN=RIGHT>2,007,047</TD><TD ALIGN=RIGHT>3,888,476</TD><TD ALIGN=RIGHT>1,205,466</TD><TD ALIGN=RIGHT>1,192,784</TD><TD ALIGN=RIGHT>12,682</TD><TD ALIGN=RIGHT>% 1.05</TD></TR> <TR><TH ALIGN=LEFT><A HREF="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" TARGET="_blank">WI2</A></TH><TD ALIGN=RIGHT>1,122,564</TD><TD ALIGN=RIGHT>2,298,885</TD><TD ALIGN=RIGHT>589,547</TD><TD ALIGN=RIGHT>582,843</TD><TD ALIGN=RIGHT>6,704</TD><TD ALIGN=RIGHT>% 1.14</TD></TR> <TR><TH ALIGN=LEFT><A HREF="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" TARGET="_blank">ABC12</A></TH><TD ALIGN=RIGHT>1,120,939</TD><TD ALIGN=RIGHT>2,169,280</TD><TD ALIGN=RIGHT>778,216</TD><TD ALIGN=RIGHT>771,827</TD><TD ALIGN=RIGHT>6,389</TD><TD ALIGN=RIGHT>0.82</TD></TR> <TR><TH ALIGN=LEFT><A HREF="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" TARGET="_blank">ABC7</A></TH><TD ALIGN=RIGHT>1,116,966</TD><TD ALIGN=RIGHT>2,152,975</TD><TD ALIGN=RIGHT>650,329</TD><TD ALIGN=RIGHT>644,071</TD><TD ALIGN=RIGHT>6,258</TD><TD ALIGN=RIGHT>0.96</TD></TR> <TR><TH ALIGN=LEFT><A HREF="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" TARGET="_blank">ABC9</A></TH><TD ALIGN=RIGHT>1,065,503</TD><TD ALIGN=RIGHT>2,084,892</TD><TD ALIGN=RIGHT>757,644</TD><TD ALIGN=RIGHT>750,648</TD><TD ALIGN=RIGHT>6,996</TD><TD ALIGN=RIGHT>0.92</TD></TR> <TR><TH ALIGN=LEFT><A HREF="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" TARGET="_blank">ABC10</A></TH><TD ALIGN=RIGHT>1,062,082</TD><TD ALIGN=RIGHT>2,121,489</TD><TD ALIGN=RIGHT>788,344</TD><TD ALIGN=RIGHT>781,331</TD><TD ALIGN=RIGHT>7,013</TD><TD ALIGN=RIGHT>0.89</TD></TR> <TR><TH ALIGN=LEFT><A HREF="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" TARGET="_blank">ABC14</A></TH><TD ALIGN=RIGHT>1,042,929</TD><TD ALIGN=RIGHT>2,089,193</TD><TD ALIGN=RIGHT>846,055</TD><TD ALIGN=RIGHT>839,126</TD><TD ALIGN=RIGHT>6,929</TD><TD ALIGN=RIGHT>0.82</TD></TR> <TR><TH ALIGN=LEFT><A HREF="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" TARGET="_blank">ABC13</A></TH><TD ALIGN=RIGHT>1,009,643</TD><TD ALIGN=RIGHT>2,057,345</TD><TD ALIGN=RIGHT>811,829</TD><TD ALIGN=RIGHT>803,589</TD><TD ALIGN=RIGHT>8,240</TD><TD ALIGN=RIGHT>1.01</TD></TR> <TR><TH ALIGN=LEFT><A HREF="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" TARGET="_blank">ABC11</A></TH><TD ALIGN=RIGHT>998,880</TD><TD ALIGN=RIGHT>1,966,644</TD><TD ALIGN=RIGHT>730,565</TD><TD ALIGN=RIGHT>724,864</TD><TD ALIGN=RIGHT>5,701</TD><TD ALIGN=RIGHT>0.78</TD></TR> <TR><TH ALIGN=LEFT><A HREF="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" TARGET="_blank">ABC23</A></TH><TD ALIGN=RIGHT>942,133</TD><TD ALIGN=RIGHT>1,535,766</TD><TD ALIGN=RIGHT>437,098</TD><TD ALIGN=RIGHT>433,896</TD><TD ALIGN=RIGHT>3,202</TD><TD ALIGN=RIGHT>0.73</TD></TR> <TR><TH ALIGN=LEFT><A HREF="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" TARGET="_blank">ABC16</A></TH><TD ALIGN=RIGHT>907,948</TD><TD ALIGN=RIGHT>1,534,288</TD><TD ALIGN=RIGHT>452,316</TD><TD ALIGN=RIGHT>449,101</TD><TD ALIGN=RIGHT>3,215</TD><TD ALIGN=RIGHT>0.71</TD></TR> <TR><TH ALIGN=LEFT><A HREF="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" TARGET="_blank">ABC24</A></TH><TD ALIGN=RIGHT>835,600</TD><TD ALIGN=RIGHT>1,383,475</TD><TD ALIGN=RIGHT>399,056</TD><TD ALIGN=RIGHT>395,776</TD><TD ALIGN=RIGHT>3,280</TD><TD ALIGN=RIGHT>0.82</TD></TR> <TR><TH ALIGN=LEFT><A HREF="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" TARGET="_blank">ABC27</A></TH><TD ALIGN=RIGHT>768,336</TD><TD ALIGN=RIGHT>1,229,804</TD><TD ALIGN=RIGHT>334,232</TD><TD ALIGN=RIGHT>331,822</TD><TD ALIGN=RIGHT>2,410</TD><TD ALIGN=RIGHT>0.72</TD></TR> <TR><TH ALIGN=LEFT><A HREF="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" TARGET="_blank">ABC18</A></TH><TD ALIGN=RIGHT>743,640</TD><TD ALIGN=RIGHT>1,204,811</TD><TD ALIGN=RIGHT>325,150</TD><TD ALIGN=RIGHT>322,904</TD><TD ALIGN=RIGHT>2,246</TD><TD ALIGN=RIGHT>0.69</TD></TR> <TR><TH ALIGN=LEFT><A HREF="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" TARGET="_blank">COR2A</A></TH><TD ALIGN=RIGHT>723,569</TD><TD ALIGN=RIGHT>1,441,881</TD><TD ALIGN=RIGHT>583,327</TD><TD ALIGN=RIGHT>578,578</TD><TD ALIGN=RIGHT>4,749</TD><TD ALIGN=RIGHT>0.81</TD></TR> <TR><TH ALIGN=LEFT><A HREF="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" TARGET="_blank">ABC22</A></TH><TD ALIGN=RIGHT>519,274</TD><TD ALIGN=RIGHT>780,151</TD><TD ALIGN=RIGHT>189,988</TD><TD ALIGN=RIGHT>188,743</TD><TD ALIGN=RIGHT>1,245</TD><TD ALIGN=RIGHT>0.66</TD></TR> <TR><TH ALIGN=LEFT><A HREF="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" TARGET="_blank">ABC21</A></TH><TD ALIGN=RIGHT>436,930</TD><TD ALIGN=RIGHT>680,160</TD><TD ALIGN=RIGHT>182,214</TD><TD ALIGN=RIGHT>180,973</TD><TD ALIGN=RIGHT>1,241</TD><TD ALIGN=RIGHT>0.68</TD></TR> <TR><TH ALIGN=LEFT><A HREF="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" TARGET="_blank">RP11</A></TH><TD ALIGN=RIGHT>292,975</TD><TD ALIGN=RIGHT>394,813</TD><TD ALIGN=RIGHT>86,875</TD><TD ALIGN=RIGHT>85,903</TD><TD ALIGN=RIGHT>972</TD><TD ALIGN=RIGHT>1.12</TD></TR> <TR><TH ALIGN=LEFT><A HREF="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" TARGET="_blank">COR02</A></TH><TD ALIGN=RIGHT>272,396</TD><TD ALIGN=RIGHT>546,984</TD><TD ALIGN=RIGHT>208,377</TD><TD ALIGN=RIGHT>206,782</TD><TD ALIGN=RIGHT>1,595</TD><TD ALIGN=RIGHT>0.77</TD></TR> <TR><TH ALIGN=LEFT><A HREF="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" TARGET="_blank">CTD</A></TH><TD ALIGN=RIGHT>226,848</TD><TD ALIGN=RIGHT>403,688</TD><TD ALIGN=RIGHT>96,594</TD><TD ALIGN=RIGHT>94,941</TD><TD ALIGN=RIGHT>1,653</TD><TD ALIGN=RIGHT>1.71</TD></TR> <TR><TH ALIGN=LEFT><A HREF="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" TARGET="_blank">CH17</A></TH><TD ALIGN=RIGHT>176,209</TD><TD ALIGN=RIGHT>325,659</TD><TD ALIGN=RIGHT>105,805</TD><TD ALIGN=RIGHT>105,060</TD><TD ALIGN=RIGHT>745</TD><TD ALIGN=RIGHT>0.70</TD></TR> <TR><TH ALIGN=LEFT><A HREF="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" TARGET="_blank">ABC20</A></TH><TD ALIGN=RIGHT>49,132</TD><TD ALIGN=RIGHT>80,350</TD><TD ALIGN=RIGHT>24,720</TD><TD ALIGN=RIGHT>24,474</TD><TD ALIGN=RIGHT>246</TD><TD ALIGN=RIGHT>1.00</TD></TR> <TR><TH ALIGN=LEFT>UCSC<BR>dropped</TH><TD ALIGN=RIGHT>152,979</TD><TD ALIGN=RIGHT>n/a</TD><TD ALIGN=RIGHT>n/a</TD><TD ALIGN=RIGHT>n/a</TD><TD ALIGN=RIGHT>n/a</TD><TD ALIGN=RIGHT>n/a</TD></TR> <TR><TH ALIGN=LEFT>multiple<BR>mappings</TH><TD ALIGN=RIGHT>775,629</TD><TD ALIGN=RIGHT>n/a</TD><TD ALIGN=RIGHT>n/a</TD><TD ALIGN=RIGHT>n/a</TD><TD ALIGN=RIGHT>n/a</TD><TD ALIGN=RIGHT>n/a</TD></TR> </TABLE> </P> <H2>Credits</H2> <P> +Many of the libraries shown here were constructed by +<A HREF="https://bacpacresources.org/" TARGET="_blank">Pieter J. de Jong</A> +and colleagues, including the RPCI-11 (RP11) library at the Roswell Park +Cancer Institute, and the CHORI-17 (CH17) and BCGSC 32k Re-Array libraries +at BACPAC Genomics (formerly at the Children's Hospital Oakland Research +Institute, CHORI). For background on de Jong's role in building these +clone libraries, see this +<A HREF="https://undark.org/2024/07/09/informed-consent-human-genome-project/" +TARGET="_blank">Undark profile</A>.</P> +<P> Additional information about the clone, including how it can be obtained, may be found at the <A HREF="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" -TARGET=_blank>NCBI Clone Registry</A>. To view the registry entry for a +TARGET="_blank">NCBI Clone Registry</A>. To view the registry entry for a specific clone, open the details page for the clone and click on its name at the top of the page.</P>