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net-format.scroll
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net-format.scroll
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import ../code/conceptPage.scroll
id net-format
name net-format
appeared 2006
tags textDataFormat
conceptDescription The net file format is used to describe the axtNet data that underlie the net alignment annotations in the Genome Browser. In 2016 it was revised so that line indentation level represents the parent/child relationship between records and is a necessary part of the net file format. Child records are indented one space from the parent, as shown in the example net file below.
fileType text
centralPackageRepositoryCount 0
country United States
originCommunity University of California, Santa Cruz
reference https://genome.ucsc.edu/goldenPath/help/net.html
example
net chr2L 23011544
fill 6004 3278 chrXR_group3a - 1396397 2164 id 25606 score 23114 ali 782 qDup 576 type top tN 0 qN 0 tR 36 qR 0 tTrf 0 qTrf 0
gap 6065 2 chrXR_group3a - 1398498 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0
gap 6096 1485 chrXR_group3a - 1397572 897 tN 0 qN 0 tR 36 qR 0 tTrf 0 qTrf 0
fill 6096 513 chrU - 5570675 533 id 48675 score 4435 ali 465 qDup 533 type nonSyn tN 0 qN 0 tR 0 qR 13 tTrf 0 qTrf 0
gap 6116 8 chrU - 5571188 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0
gap 6156 5 chrU - 5571156 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0
gap 6184 3 chrU - 5571133 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0
gap 6212 18 chrU - 5571106 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0
gap 6244 9 chrU - 5571092 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0
gap 6340 2 chrU - 5570996 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0
gap 6515 3 chrU - 5570771 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0
gap 7623 1 chrXR_group3a - 1397530 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0
gap 7664 1007 chrXR_group3a - 1397008 482 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0
fill 7664 382 chrXL_group1e - 8262003 506 id 25608 score 10609 ali 364 qDup 506 type nonSyn tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0
gap 7784 4 chrXL_group1e - 8262361 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0
gap 7792 3 chrXL_group1e - 8262357 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0
gap 7921 2 chrXL_group1e - 8262126 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0
gap 7949 9 chrXL_group1e - 8262092 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0
gap 8693 1 chrXR_group3a - 1396985 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0
fill 9833 1251 chrU - 5562980 1239 id 48675 score 10720 ali 1124 qDup 1094 type top tN 0 qN 0 tR 22 qR 88 tTrf 0 qTrf 0
gap 9966 7 chrU - 5564075 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0
gap 10015 3 chrU - 5564030 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0
gap 10088 2 chrU - 5563957 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0
gap 10101 8 chrU - 5563946 0 tN 0 qN 0 tR 0 qR 0 tTrf 0 qTrf 0
hasSemanticIndentation true