# No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini
# Georgios Koutsovoulos[1], Sujai Kumar[1], Dominik Laetsch[1,2], Jennifer Daub[1], Claire Conlon[1], Habib Maroon[1], Fran Thomas[1], Lewis Stevens[1], Aziz Aboobaker[3], and Mark Blaxter[1]*
# 1 Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
# 2 The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
# 3 Department of Zoology, University of Oxford, South Parks Road, Oxford OX, UK.
# * Corresponding author mark.blaxter@ed.ac.uk

# Supplemental_File_4_Assignments_of_the_6663_putative_UNC_HGT_loci

# Assignment of genes predicted by Boothby et al as HGT candidates in this analysis.
# Each column scores each gene 1 or 0 for whether it meets or does not meet each criterion.
# UNC_hgt_gene_id - the UNC gene ID taken from their Supplemental Information file Boothbysuppinfo_pnas.201510461SI
# covlt10 - coverage of genomic reads less than 10 in either UNC or Edinburgh raw data
# noneuk - all the genes with sequence similarity to NCBI nr are classified as non-eukaryotic
# onlynoneuk - all the genes are classified as non-eukaryotic by sequence similarity to NCBI nr
# tpmlt01 - expression, measured as transcripts per million, of <0.1
# blobbac - identified as bacterial in the blobplot analysis
# noNRhit - no NR BLAST hit (a hit is considered where at least 70% of the query HGT protein matches any NR entry with an evalue cutoff of 1e-5) 

#UNC_hgt_gene_id	covlt10	noneuk	onlynoneuk	tpmlt01	blobbac	noNRhit
snap_masked-scaffold13609_size6909-processed-gene-0.13	1	1	0	1	1	1
snap_masked-scaffold13334_size7077-processed-gene-0.4	1	1	0	1	1	1
snap_masked-scaffold4241_size15856-processed-gene-0.18	1	1	0	1	1	1
snap_masked-scaffold7971_size10521-processed-gene-0.10	1	1	0	1	1	1
snap_masked-scaffold16178_size5466-processed-gene-0.6	1	1	1	1	1	1
snap_masked-scaffold6541_size12033-processed-gene-0.0	1	0	0	1	1	1
snap_masked-scaffold11161_size8406-processed-gene-0.3	1	1	1	1	1	1
augustus_masked-scaffold23457_size2694-processed-gene-0.0	1	1	1	1	1	1
augustus_masked-scaffold6264_size12380-processed-gene-0.2	1	1	1	1	0	1
maker-scaffold1099_size30813-snap-gene-0.32	1	1	1	1	1	1
snap_masked-scaffold2188_size22401-processed-gene-0.10	1	1	1	1	1	1
snap_masked-scaffold10739_size8636-processed-gene-0.10	1	1	1	1	1	1
snap_masked-scaffold10986_size8495-processed-gene-0.0	1	1	1	1	1	1
snap_masked-scaffold16630_size5246-processed-gene-0.1	1	0	0	1	0	1
snap_masked-scaffold16484_size5318-processed-gene-0.0	1	1	1	1	1	1
snap_masked-scaffold20692_size3574-processed-gene-0.2	1	1	0	1	1	1
snap_masked-scaffold6996_size11515-processed-gene-0.6	1	1	1	1	1	1
augustus_masked-scaffold8652_size9993-processed-gene-0.3	1	1	0	1	1	1
snap_masked-scaffold1333_size28282-processed-gene-0.14	1	1	1	1	1	1
snap_masked-scaffold18545_size4397-processed-gene-0.5	1	1	0	1	1	1
snap_masked-scaffold5328_size13840-processed-gene-0.15	1	1	0	1	1	1
maker-scaffold22432_size3005-snap-gene-0.4	1	1	1	1	1	1
maker-scaffold3943_size16644-snap-gene-0.19	1	1	1	1	1	1
augustus_masked-scaffold17875_size4688-processed-gene-0.1	1	1	1	1	1	1
maker-scaffold23568_size2664-snap-gene-0.6	1	1	1	1	1	1
snap_masked-scaffold1143_size30362-processed-gene-0.26	1	1	1	1	1	1
maker-scaffold544_size41181-augustus-gene-0.37	1	1	1	1	1	1
snap_masked-scaffold22490_size2989-processed-gene-0.4	1	1	1	1	1	1
augustus_masked-scaffold8740_size9920-processed-gene-0.6	1	1	1	1	1	1
snap_masked-scaffold7017_size11493-processed-gene-0.8	1	1	1	1	1	1
snap_masked-scaffold5814_size13058-processed-gene-0.0	1	1	1	1	1	1
maker-scaffold7420_size11047-snap-gene-0.6	1	1	1	1	1	1
maker-scaffold24857_size2323-snap-gene-0.5	1	1	1	1	1	1
maker-scaffold12267_size7740-snap-gene-0.15	1	1	0	1	1	1
snap_masked-scaffold2367_size21676-processed-gene-0.19	1	1	0	1	1	1
snap_masked-scaffold25301_size2220-processed-gene-0.2	1	1	1	1	1	1
snap_masked-scaffold495_size42901-processed-gene-0.20	1	1	1	1	1	1
snap_masked-scaffold331_size50517-processed-gene-0.42	1	1	1	1	1	1
augustus_masked-scaffold419_size45809-processed-gene-0.3	1	1	0	1	1	1
maker-scaffold22678_size2926-snap-gene-0.5	1	1	1	1	1	1
maker-scaffold12921_size7325-augustus-gene-0.13	1	1	1	1	1	1
augustus_masked-scaffold11798_size8043-processed-gene-0.4	1	1	1	1	1	1
maker-scaffold1143_size30362-snap-gene-0.39	1	1	1	1	1	1
snap_masked-scaffold13557_size6938-processed-gene-0.6	1	1	1	1	1	1
snap_masked-scaffold6105_size12614-processed-gene-0.10	1	1	1	1	1	1
augustus_masked-scaffold22711_size2913-processed-gene-0.0	1	1	1	1	1	1
augustus_masked-scaffold25411_size2194-processed-gene-0.0	1	1	1	1	1	1
maker-scaffold18084_size4598-augustus-gene-0.5	1	1	1	1	1	1
maker-scaffold8656_size9988-augustus-gene-0.12	1	1	1	1	1	1
maker-scaffold16231_size5441-snap-gene-0.6	1	1	1	1	1	1
snap_masked-scaffold5215_size14019-processed-gene-0.13	1	1	0	1	1	1
snap_masked-scaffold10487_size8781-processed-gene-0.8	1	1	1	1	1	1
augustus_masked-scaffold9632_size9290-processed-gene-0.5	1	1	1	1	1	1
maker-scaffold7_size968285-snap-gene-3.61	1	1	1	1	1	1
snap_masked-scaffold10365_size8849-processed-gene-0.16	1	1	1	1	1	1
snap_masked-scaffold13005_size7274-processed-gene-0.10	1	1	1	1	1	1
snap_masked-scaffold9104_size9656-processed-gene-0.2	1	1	1	1	1	1
snap_masked-scaffold19385_size4051-processed-gene-0.5	1	1	1	1	1	1
snap_masked-scaffold2331_size21791-processed-gene-0.20	1	1	1	1	1	1
snap_masked-scaffold48_size118896-processed-gene-0.95	1	1	1	1	1	1
augustus_masked-scaffold19208_size4136-processed-gene-0.1	1	1	1	1	1	1
augustus_masked-scaffold380_size47716-processed-gene-0.4	1	1	0	1	1	1
snap_masked-scaffold11137_size8420-processed-gene-0.5	1	1	1	1	1	1
augustus_masked-scaffold21881_size3187-processed-gene-0.0	1	0	0	1	0	1
snap_masked-scaffold601_size39493-processed-gene-0.31	1	1	1	1	1	1
augustus_masked-scaffold6364_size12235-processed-gene-0.0	1	1	1	1	1	1
maker-scaffold15635_size5740-snap-gene-0.7	1	1	1	1	1	1
snap_masked-scaffold11917_size7953-processed-gene-0.4	1	1	1	1	1	1
augustus_masked-scaffold7120_size11393-processed-gene-0.3	1	1	1	1	1	1
snap_masked-scaffold2349_size21735-processed-gene-0.7	1	1	1	1	1	1
snap_masked-scaffold9676_size9256-processed-gene-0.0	1	1	1	1	1	1
maker-scaffold25512_size2171-snap-gene-0.5	1	1	1	1	1	1
snap_masked-scaffold1079_size31058-processed-gene-0.19	1	1	1	1	1	1
snap_masked-scaffold17753_size4736-processed-gene-0.4	1	1	1	1	1	1
maker-scaffold14329_size6465-augustus-gene-0.12	1	0	0	1	0	1
snap_masked-scaffold11597_size8157-processed-gene-0.11	1	1	1	1	1	1
snap_masked-scaffold309_size52076-processed-gene-0.8	1	1	1	1	1	1
maker-scaffold24340_size2450-snap-gene-0.3	1	1	1	1	1	1
snap_masked-scaffold10744_size8630-processed-gene-0.0	1	1	1	1	1	1
snap_masked-scaffold126_size77140-processed-gene-0.40	1	1	0	1	1	1
snap_masked-scaffold23131_size2788-processed-gene-0.3	1	1	1	1	1	1
snap_masked-scaffold4495_size15350-processed-gene-0.9	1	1	1	1	1	1
maker-scaffold8785_size9885-snap-gene-0.14	1	1	1	1	1	1
snap_masked-scaffold20271_size3721-processed-gene-0.3	1	1	1	1	1	1
snap_masked-scaffold22910_size2856-processed-gene-0.4	1	1	1	1	1	1
maker-scaffold10593_size8718-snap-gene-0.1	1	1	1	1	1	1
snap_masked-scaffold12104_size7845-processed-gene-0.5	1	1	1	1	1	1
snap_masked-scaffold9659_size9272-processed-gene-0.10	1	1	1	1	1	1
maker-scaffold13141_size7198-snap-gene-0.12	1	1	1	1	1	1
augustus_masked-scaffold1702_size25250-processed-gene-0.11	1	1	1	1	1	1
augustus_masked-scaffold8406_size10178-processed-gene-0.4	1	1	1	1	1	1
maker-scaffold22640_size2938-snap-gene-0.3	1	1	1	1	1	1
snap_masked-scaffold16983_size5083-processed-gene-0.4	1	1	1	1	1	1
snap_masked-scaffold8758_size9903-processed-gene-0.7	1	1	1	1	1	1
augustus_masked-scaffold2171_size22471-processed-gene-0.9	1	1	0	1	1	1
augustus_masked-scaffold12281_size7734-processed-gene-0.3	1	1	1	1	1	1
augustus_masked-scaffold3943_size16644-processed-gene-0.4	1	1	1	1	1	1
augustus_masked-scaffold84_size92828-processed-gene-0.12	1	1	0	1	1	1
maker-scaffold26238_size2008-snap-gene-0.6	1	1	1	1	1	1
maker-scaffold18363_size4480-augustus-gene-0.6	1	1	1	1	1	1
snap_masked-scaffold13487_size6978-processed-gene-0.4	1	1	1	1	1	1
snap_masked-scaffold13800_size6794-processed-gene-0.7	1	1	1	1	1	1
maker-scaffold12335_size7695-snap-gene-0.13	1	1	1	1	1	1
snap_masked-scaffold37_size133809-processed-gene-0.79	1	0	0	1	1	1
augustus_masked-scaffold25463_size2182-processed-gene-0.1	1	1	1	1	1	1
maker-scaffold12475_size7605-augustus-gene-0.12	1	1	1	1	1	1
maker-scaffold613_size39278-snap-gene-0.30	1	1	0	1	1	1
snap_masked-scaffold9086_size9668-processed-gene-0.0	1	1	1	1	1	1
augustus_masked-scaffold446_size44484-processed-gene-0.15	1	1	0	1	1	1
augustus_masked-scaffold613_size39278-processed-gene-0.10	1	1	0	1	1	1
snap_masked-scaffold21535_size3297-processed-gene-0.0	1	1	1	1	1	1
snap_masked-scaffold4384_size15564-processed-gene-0.1	1	1	0	1	1	1
snap_masked-scaffold6727_size11808-processed-gene-0.1	1	1	1	1	1	1
snap_masked-scaffold1146_size30319-processed-gene-0.11	1	1	1	1	1	1
snap_masked-scaffold309_size52076-processed-gene-0.7	1	1	1	1	1	1
maker-scaffold7146_size11364-snap-gene-0.13	1	1	1	1	1	1
augustus_masked-scaffold15451_size5834-processed-gene-0.3	1	1	1	1	1	1
augustus_masked-scaffold21264_size3384-processed-gene-0.1	1	1	1	1	1	1
augustus_masked-scaffold4374_size15587-processed-gene-0.3	1	1	1	1	1	1
augustus_masked-scaffold6799_size11729-processed-gene-0.1	1	1	1	1	1	1
maker-scaffold13141_size7198-augustus-gene-0.11	1	1	1	1	1	1
snap_masked-scaffold17604_size4798-processed-gene-0.5	1	1	1	1	1	1
maker-scaffold12508_size7583-snap-gene-0.9	1	1	1	1	1	1
maker-scaffold8649_size9996-snap-gene-0.13	1	1	1	1	1	1
snap_masked-scaffold11489_size8215-processed-gene-0.1	1	1	1	1	1	1
snap_masked-scaffold1966_size23550-processed-gene-0.20	1	1	1	1	1	1
snap_masked-scaffold6546_size12028-processed-gene-0.14	1	1	1	1	1	1
augustus_masked-scaffold13567_size6933-processed-gene-0.1	1	1	1	1	1	1
maker-scaffold813_size34939-augustus-gene-0.47	1	1	0	1	1	1
snap_masked-scaffold331_size50517-processed-gene-0.49	1	1	1	1	1	1
maker-scaffold9151_size9618-snap-gene-0.10	1	1	0	1	1	1
snap_masked-scaffold1040_size31561-processed-gene-0.16	1	0	0	1	0	1
maker-scaffold13017_size7270-snap-gene-0.5	1	1	1	1	1	1
maker-scaffold1040_size31561-augustus-gene-0.29	1	0	0	1	0	1
snap_masked-scaffold1571_size26160-processed-gene-0.18	1	1	1	1	1	1
snap_masked-scaffold3_size1208507-processed-gene-0.40	1	0	0	1	1	1
maker-scaffold10846_size8570-augustus-gene-0.12	1	1	1	1	1	1
snap_masked-scaffold14434_size6399-processed-gene-0.0	1	1	1	1	1	1
augustus_masked-scaffold10334_size8865-processed-gene-0.4	1	1	1	1	1	1
augustus_masked-scaffold1657_size25561-processed-gene-0.1	1	1	1	1	1	1
maker-scaffold18372_size4477-augustus-gene-0.10	1	1	1	1	1	1
snap_masked-scaffold13939_size6702-processed-gene-0.6	1	1	1	1	1	1
maker-scaffold16563_size5278-augustus-gene-0.8	1	1	1	1	1	1
maker-scaffold10_size447749-snap-gene-2.50	1	1	1	1	1	1
maker-scaffold2606_size20604-augustus-gene-0.28	1	1	0	1	1	1
maker-scaffold13151_size7193-snap-gene-0.14	1	1	1	1	1	1
augustus_masked-scaffold14924_size6118-processed-gene-0.0	1	1	1	1	1	1
augustus_masked-scaffold1633_size25747-processed-gene-0.7	1	1	1	1	1	1
maker-scaffold10172_size8941-snap-gene-0.19	1	1	1	1	1	1
maker-scaffold331_size50517-augustus-gene-0.58	1	1	1	1	1	1
snap_masked-scaffold11126_size8426-processed-gene-0.10	1	1	1	1	1	1
snap_masked-scaffold7956_size10532-processed-gene-0.5	1	1	1	1	1	1
maker-scaffold5200_size14048-snap-gene-0.9	1	1	1	1	1	1
snap_masked-scaffold380_size47716-processed-gene-0.17	1	1	0	1	1	1
snap_masked-scaffold7030_size11484-processed-gene-0.9	1	1	1	1	1	1
snap_masked-scaffold5831_size13032-processed-gene-0.0	1	1	1	1	1	1
maker-scaffold18962_size4231-augustus-gene-0.3	1	1	1	1	1	1
maker-scaffold23467_size2691-snap-gene-0.6	1	1	1	1	1	1
maker-scaffold2745_size20166-augustus-gene-0.21	1	1	1	1	1	1
snap_masked-scaffold11384_size8274-processed-gene-0.10	1	1	1	1	1	1
snap_masked-scaffold8330_size10231-processed-gene-0.7	1	1	1	1	1	1
maker-scaffold15025_size6065-snap-gene-0.5	1	1	1	1	1	1
augustus_masked-scaffold23025_size2822-processed-gene-0.1	1	1	1	1	1	1
augustus_masked-scaffold8037_size10470-processed-gene-0.2	1	1	1	1	1	1
maker-scaffold17575_size4812-snap-gene-0.5	1	1	1	1	1	1
maker-scaffold4884_size14601-snap-gene-0.20	1	1	1	1	1	1
snap_masked-scaffold403_size46502-processed-gene-0.22	1	1	1	1	1	1
snap_masked-scaffold2777_size20057-processed-gene-0.15	1	1	1	1	1	1
augustus_masked-scaffold11312_size8321-processed-gene-0.5	1	1	1	1	1	1
augustus_masked-scaffold13110_size7219-processed-gene-0.1	1	1	1	1	1	1
augustus_masked-scaffold15174_size5975-processed-gene-0.1	1	1	1	1	1	1
augustus_masked-scaffold16171_size5469-processed-gene-0.2	1	1	1	1	1	1
maker-scaffold17854_size4695-snap-gene-0.7	1	1	1	1	1	1
snap_masked-scaffold9650_size9277-processed-gene-0.3	1	1	1	1	1	1
augustus_masked-scaffold1107_size30746-processed-gene-0.10	1	1	1	1	1	1
augustus_masked-scaffold13266_size7125-processed-gene-0.4	1	1	0	1	1	1
augustus_masked-scaffold4613_size15117-processed-gene-0.7	1	1	1	1	1	1
augustus_masked-scaffold1499_size26805-processed-gene-0.6	1	1	1	1	1	1
augustus_masked-scaffold9111_size9649-processed-gene-0.0	1	1	1	1	1	1
snap_masked-scaffold406_size46217-processed-gene-0.33	1	1	1	1	1	1
snap_masked-scaffold7243_size11266-processed-gene-0.4	1	1	1	1	1	1
maker-scaffold24204_size2484-augustus-gene-0.4	1	1	1	1	1	1
augustus_masked-scaffold12673_size7473-processed-gene-0.3	1	1	1	1	1	1
maker-scaffold4718_size14934-augustus-gene-0.27	1	1	1	1	1	1
augustus_masked-scaffold3423_size18017-processed-gene-0.7	1	1	1	1	1	1
snap_masked-scaffold16908_size5120-processed-gene-0.5	1	1	1	1	1	1
snap_masked-scaffold5934_size12884-processed-gene-0.14	1	1	1	1	1	1
snap_masked-scaffold8017_size10488-processed-gene-0.3	1	1	1	1	1	1
maker-scaffold18562_size4389-snap-gene-0.9	1	1	1	1	1	1
snap_masked-scaffold18084_size4598-processed-gene-0.2	1	1	1	1	1	1
augustus_masked-scaffold12199_size7786-processed-gene-0.3	1	1	1	1	1	1
augustus_masked-scaffold16355_size5385-processed-gene-0.3	1	1	1	1	1	1
maker-scaffold25426_size2191-snap-gene-0.4	1	1	1	1	1	1
snap_masked-scaffold5094_size14218-processed-gene-0.4	1	1	1	1	1	1
snap_masked-scaffold7138_size11375-processed-gene-0.10	1	1	1	1	1	1
snap_masked-scaffold15592_size5762-processed-gene-0.2	1	1	1	1	1	1
snap_masked-scaffold6852_size11677-processed-gene-0.2	1	1	1	1	1	1
augustus_masked-scaffold3197_size18679-processed-gene-0.3	1	1	1	1	1	1
augustus_masked-scaffold3912_size16746-processed-gene-0.2	1	1	1	1	1	1
maker-scaffold14435_size6399-augustus-gene-0.7	1	1	1	1	1	1
maker-scaffold18000_size4632-snap-gene-0.6	1	1	1	1	1	1
snap_masked-scaffold14903_size6129-processed-gene-0.0	1	1	1	1	1	1
augustus_masked-scaffold21085_size3439-processed-gene-0.0	1	1	1	1	1	1
augustus_masked-scaffold3_size1208507-processed-gene-5.11	1	0	0	1	1	1
snap_masked-scaffold192_size64333-processed-gene-0.35	1	1	0	1	1	1
augustus_masked-scaffold10963_size8507-processed-gene-0.3	1	1	1	1	1	1
snap_masked-scaffold21256_size3386-processed-gene-0.3	1	1	1	1	1	1
snap_masked-scaffold2284_size21998-processed-gene-0.10	1	1	1	1	1	1
augustus_masked-scaffold3058_size19117-processed-gene-0.2	1	1	1	1	1	1
snap_masked-scaffold10963_size8507-processed-gene-0.6	1	1	1	1	1	1
snap_masked-scaffold21250_size3389-processed-gene-0.4	1	1	1	1	1	1
snap_masked-scaffold8686_size9966-processed-gene-0.16	1	1	1	1	1	1
maker-scaffold21804_size3211-snap-gene-0.9	1	1	0	1	1	1
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