8c2f7318d8d821de9b2a25750586a94ab5e8c1bb
lrnassar
Fri Nov 15 18:50:19 2024 -0800
Giving the UI link cronjob some love by fixing all the 301 redirects. These are the bulk of the items listed on the cron. No RM.
diff --git src/hg/makeDb/trackDb/human/ntModernHumans.html src/hg/makeDb/trackDb/human/ntModernHumans.html
index a2b93cf..ba4eb8d 100644
--- src/hg/makeDb/trackDb/human/ntModernHumans.html
+++ src/hg/makeDb/trackDb/human/ntModernHumans.html
@@ -18,50 +18,50 @@
TARGET=_blank>SAM Format Specification
for more information on the SAM/BAM file format). If a query sequence was
originally the reverse of what has been stored and aligned, it will have the
following
flag:
(0x10) Read is on '-' strand.
BAM/SAM alignment representations also have tags. Some tags are predefined and others (those beginning
with X, Y or Z) are defined by the aligner or data submitter.
The following is a list of the tags associated with this track. For this
track, those starting with X are specific to the
-Burrows-Wheeler Aligner (BWA).
-- XT: Type: Unique/Repeat/N/Mate-sw
- NM: Number of nucleotide differences (i.e. edit distance to the reference sequence)
- SM: Mapping quality if the read is mapped as a single read rather than as a read pair
- AM: Smaller single-end mapping quality of the two reads in a pair
-- X0: Number of best hits
-- X1: Number of suboptimal hits found by BWA
-- XM: Number of mismatches in the alignment
-- XO: Number of gap opens
-- XG: Number of gap extentions
- MD: String for mismatching positions in the format of [0-9]+(([ACGTN]|\^[ACGTN]+)[0-9]+)*
The item labels and display colors of features within this track can be
configured through the controls at the top of the track description page.
- Display Read Names: By default, read names are not displayed. To
display the read names, selected the check box next to "Display read names".
@@ -97,31 +97,31 @@
When "unpaired ends" is selected, items that were paired in
sequencing but whose mate was not mapped are colored gray, while singletons
and properly paired items are black. Alignment quality is the default.
Methods
The genomes of a San individual from Southern Africa (HGDP01029), a Yoruba
individual from West Africa (HGDP00927), a Han Chinese individual (HGDP00778),
an individual from Papua New Guinea (HGDP00542), and a French individual
(HGDP00521) from Western Europe were sequenced to 4- to 6-fold coverage on
the Illumina GAII platform. These sequences were aligned to the human
-reference genome (NCBI36/hg18) using the Burrows-Wheeler Aligner (BWA). Reads with an alignment
quality of less than 30 were not included in these data. Those with an alignment
quality greater than or equal to 30 were analyzed using a similar approach to
that used for the Neandertal data.
Credits
This track was produced at UCSC using data generated by
Ed Green.
References