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Added Ara-3 genomes
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jeffreybarrick committed Dec 17, 2017
1 parent 21583e9 commit 79352db
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2 changes: 2 additions & 0 deletions .gitignore
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summary/*
csv/*
curation/*
fasta/*
*-annotated/*
shiny/LTEE-clone-curated.tsv
55 changes: 26 additions & 29 deletions LTEE-clone-curated/Ara-3_10000gen_4538A.gd
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#=GENOME_DIFF 1.0
#=TITLE Ara-3_10000gen_4538A
#=AUTHOR Deatherage, Daniel
#=TIME 10000
#=POPULATION Ara-3
#=TREATMENT LTEE
#=CLONE A
#=MUTATOR_STATUS non-mutator
#=REFSEQ https://raw.githubusercontent.com/barricklab/LTEE/7da91974eafac0c5a8f903ae57275795d4395af2/reference/REL606.gbk
#=READSEQ ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR258/005/SRR2589045/SRR2589045_1.fastq.gz
#=READSEQ ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR258/005/SRR2589045/SRR2589045_2.fastq.gz
DEL 1 . REL606 16989 1 adjacent=IS150 within=2:2
MOB 2 . REL606 16989 IS150 1 4
MOB 3 . REL606 78888 IS150 -1 3
SNP 4 . REL606 475173 C
MOB 5 . REL606 546191 IS1 1 9
SNP 6 . REL606 648692 T
MOB 7 . REL606 680759 IS150 1 3
DEL 8 . REL606 1270125 535 no_normalize=1
MOB 9 . REL606 1270660 IS150 -1 4
SNP 10 . REL606 1331794 A
SNP 11 . REL606 1733343 A
MOB 12 . REL606 1866486 IS150 1 3
INS 13 . REL606 2103918 CCAGCCAGCCAGCCAGCCAG repeat_length=4 repeat_new_copies=12 repeat_ref_copies=7 repeat_seq=CCAG
MOB 14 . REL606 2241332 IS150 -1 3
INS 15 . REL606 2333539 T adjacent=ISRSO11
SNP 16 . REL606 2446984 C
DEL 17 . REL606 2775878 147 mediated=IS150
SNP 18 . REL606 3339313 C
SNP 19 . REL606 3401754 A
SNP 20 . REL606 3475057 T
SNP 21 . REL606 3481820 G
DEL 22 . REL606 3895000 6460 mediated=IS150
SNP 23 . REL606 3909807 T
SNP 24 . REL606 4100183 G
MOB 25 . REL606 4110237 IS150 -1 3
DEL 26 . REL606 4431394 2
MOB 27 . REL606 4613020 IS150 1 3
MOB 1 . REL606 16990 IS150 1 3
MOB 2 . REL606 78888 IS150 -1 3
SNP 3 . REL606 475173 C
MOB 4 . REL606 546191 IS1 1 9
SNP 5 . REL606 648692 T
MOB 6 . REL606 680759 IS150 1 3
DEL 7 . REL606 1270125 535 no_normalize=1
MOB 8 . REL606 1270660 IS150 -1 4
SNP 9 . REL606 1331794 A
SNP 10 . REL606 1733343 A
MOB 11 . REL606 1866486 IS150 1 3
INS 12 . REL606 2103918 CCAGCCAGCCAGCCAGCCAG repeat_length=4 repeat_new_copies=12 repeat_ref_copies=7 repeat_seq=CCAG
MOB 13 . REL606 2241332 IS150 -1 3
INS 14 . REL606 2333539 T adjacent=ISRSO11
SNP 15 . REL606 2446984 C
DEL 16 . REL606 2775878 147 mediated=IS150
SNP 17 . REL606 3339313 C
SNP 18 . REL606 3401754 A
SNP 19 . REL606 3475057 T phylogeny_id=5
SNP 20 . REL606 3481820 G
DEL 21 . REL606 3895000 6460 mediated=IS150
SNP 22 . REL606 3909807 T
SNP 23 . REL606 4100183 G
MOB 24 . REL606 4110237 IS150 -1 3
DEL 25 . REL606 4431394 2
MOB 26 . REL606 4613020 IS150 1 3
36 changes: 36 additions & 0 deletions LTEE-clone-curated/Ara-3_10000gen_ZDB1.gd
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#=GENOME_DIFF 1.0
#=TITLE Ara-3_10000gen_ZDB1
#=TIME 10000
#=POPULATION Ara-3
#=TREATMENT LTEE
#=CLONE X
#=REFSEQ https://raw.githubusercontent.com/barricklab/LTEE/7da91974eafac0c5a8f903ae57275795d4395af2/reference/REL606.gbk
#=READSEQ BarrickLab-Private:genomes/utexas_gsaf/Project_JA13577/EQ_19_ATCACG_L005_R1_001.fastq.gz
#=READSEQ BarrickLab-Private:genomes/utexas_gsaf/Project_JA13577/EQ_19_ATCACG_L005_R2_001.fastq.gz
#=READSEQ BarrickLab-Private:genomes/utexas_gsaf/Project_JA13577/EQ_19_ATCACG_L006_R1_001.fastq.gz
#=READSEQ BarrickLab-Private:genomes/utexas_gsaf/Project_JA13577/EQ_19_ATCACG_L006_R2_001.fastq.gz
MOB 1 . REL606 16990 IS150 1 3
SNP 2 . REL606 281923 T
INS 3 . REL606 473904 GC
MOB 4 . REL606 546191 IS1 1 9
SNP 5 . REL606 648692 T
DEL 6 . REL606 1270125 535 no_normalize=1
MOB 7 . REL606 1270660 IS150 -1 4
SNP 8 . REL606 1331794 A
MOB 9 . REL606 1462320 IS150 -1 3
SNP 10 . REL606 1733343 A
INS 11 . REL606 2103918 CCAGCCAGCCAGCCAGCCAG repeat_length=4 repeat_new_copies=12 repeat_ref_copies=7 repeat_seq=CCAG
INS 12 . REL606 2333539 T
SNP 13 . REL606 2446984 C
SNP 14 . REL606 3339313 C
SNP 15 . REL606 3351741 A
SNP 16 . REL606 3401754 A
SNP 17 . REL606 3481820 G
DEL 18 . REL606 3895000 6460 mediated=IS150
SNP 19 . REL606 3909807 T
SNP 20 . REL606 4100183 G
MOB 21 . REL606 4110237 IS150 -1 3
DEL 22 . REL606 4431394 2
DEL 23 . REL606 4613020 1 adjacent=IS150 within=24:1
MOB 24 . REL606 4613020 IS150 1 3
SNP 25 . REL606 4616538 C
34 changes: 34 additions & 0 deletions LTEE-clone-curated/Ara-3_10000gen_ZDB425.gd
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#=GENOME_DIFF 1.0
#=TITLE Ara-3_10000gen_ZDB425
#=TIME 10000
#=POPULATION Ara-3
#=TREATMENT LTEE
#=CLONE Y
#=REFSEQ https://raw.githubusercontent.com/barricklab/LTEE/7da91974eafac0c5a8f903ae57275795d4395af2/reference/REL606.gbk
#=READSEQ BarrickLab-Private:genomes/utexas_gsaf/Project_JA13577/EQ_20_TGACCA_L005_R1_001.fastq.gz
#=READSEQ BarrickLab-Private:genomes/utexas_gsaf/Project_JA13577/EQ_20_TGACCA_L005_R2_001.fastq.gz
MOB 1 . REL606 16990 IS150 1 3
SNP 2 . REL606 281923 T
INS 3 . REL606 473904 GC
MOB 4 . REL606 546191 IS1 1 9
SNP 5 . REL606 648692 T
DEL 6 . REL606 1270125 535 no_normalize=1
MOB 7 . REL606 1270660 IS150 -1 4
SNP 8 . REL606 1331794 A
MOB 9 . REL606 1462320 IS150 -1 3
SNP 10 . REL606 1733343 A
INS 11 . REL606 2103918 CCAGCCAG repeat_length=4 repeat_new_copies=9 repeat_ref_copies=7 repeat_seq=CCAG
INS 12 . REL606 2333539 T
SNP 13 . REL606 2446984 C
SNP 14 . REL606 3339313 C
SNP 15 . REL606 3401754 A
SNP 16 . REL606 3481820 G
INS 17 . REL606 3893551 G phylogeny_id=3
DEL 18 . REL606 3895000 6460 mediated=IS150
SNP 19 . REL606 3909807 T
SNP 20 . REL606 4100183 G
MOB 21 . REL606 4110237 IS150 -1 3
DEL 22 . REL606 4431394 2
DEL 23 . REL606 4613020 1 adjacent=IS150 within=24:1
MOB 24 . REL606 4613020 IS150 1 3
SNP 25 . REL606 4616538 C
63 changes: 30 additions & 33 deletions LTEE-clone-curated/Ara-3_10000gen_ZDB429.gd
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#=GENOME_DIFF 1.0
#=TITLE Ara-3_10000gen_ZDB429
#=AUTHOR Barrick
#=TIME 10000
#=POPULATION Ara-3
#=TREATMENT LTEE
#=CLONE B
#=MUTATOR_STATUS non-mutator
#=REFSEQ BarrickLab-Public:release/reference/REL606.6.gbk
#=REFSEQ https://raw.githubusercontent.com/barricklab/LTEE/7da91974eafac0c5a8f903ae57275795d4395af2/reference/REL606.gbk
#=READSEQ ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR098/SRR098282/SRR098282.fastq.gz
DEL 1 . REL606 16989 1 adjacent=IS150 within=2:2
MOB 2 . REL606 16989 IS150 1 4
MOB 3 . REL606 78888 IS150 -1 3
SNP 4 . REL606 475173 C
MOB 5 . REL606 546191 IS1 1 9
SNP 6 . REL606 648692 T
MOB 7 . REL606 680759 IS150 1 3
DEL 8 . REL606 1270125 535 no_normalize=1
MOB 9 . REL606 1270660 IS150 -1 4
SNP 10 . REL606 1331794 A
INS 11 . REL606 1689712 C repeat_length=1 repeat_new_copies=7 repeat_ref_copies=6 repeat_seq=C
SNP 12 . REL606 1733343 A
MOB 13 . REL606 1866486 IS150 1 3
MOB 14 . REL606 1875544 IS186 -1 7
MOB 15 . REL606 2241332 IS150 -1 3
INS 16 . REL606 2333539 T adjacent=ISRSO11
SNP 17 . REL606 2446984 C
DEL 18 . REL606 2775878 147 mediated=IS150
SNP 19 . REL606 3339313 C
SNP 20 . REL606 3401754 A
SNP 21 . REL606 3475057 T
SNP 22 . REL606 3481820 G
DEL 23 . REL606 3895000 6460 mediated=IS150
SNP 24 . REL606 3909807 T
SNP 25 . REL606 4100183 G
MOB 26 . REL606 4110237 IS150 -1 3
MOB 27 . REL606 4415710 IS150 -1 3 phylogeny_id=1
DEL 28 . REL606 4431394 2
DEL 29 . REL606 4613020 1 adjacent=IS150 phylogeny_id=1 within=30:1
MOB 30 . REL606 4613020 IS150 1 3
MOB 1 . REL606 16990 IS150 1 3
MOB 2 . REL606 78888 IS150 -1 3
SNP 3 . REL606 475173 C
MOB 4 . REL606 546191 IS1 1 9
SNP 5 . REL606 648692 T
MOB 6 . REL606 680759 IS150 1 3
DEL 7 . REL606 1270125 535 no_normalize=1
MOB 8 . REL606 1270660 IS150 -1 4
SNP 9 . REL606 1331794 A
INS 10 . REL606 1689712 C repeat_length=1 repeat_new_copies=7 repeat_ref_copies=6 repeat_seq=C
SNP 11 . REL606 1733343 A
MOB 12 . REL606 1866486 IS150 1 3
MOB 13 . REL606 1875544 IS186 -1 7
MOB 14 . REL606 2241332 IS150 -1 3
INS 15 . REL606 2333539 T adjacent=ISRSO11
SNP 16 . REL606 2446984 C
DEL 17 . REL606 2775878 147 mediated=IS150
SNP 18 . REL606 3339313 C
SNP 19 . REL606 3401754 A
SNP 20 . REL606 3475057 T phylogeny_id=5
SNP 21 . REL606 3481820 G
DEL 22 . REL606 3895000 6460 mediated=IS150
SNP 23 . REL606 3909807 T
SNP 24 . REL606 4100183 G
MOB 25 . REL606 4110237 IS150 -1 3
MOB 26 . REL606 4415710 IS150 -1 3 phylogeny_id=1
DEL 27 . REL606 4431394 2
DEL 28 . REL606 4613020 1 adjacent=IS150 phylogeny_id=1 within=29:1
MOB 29 . REL606 4613020 IS150 1 3
2 changes: 0 additions & 2 deletions LTEE-clone-curated/Ara-3_1000gen_966A.gd
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#=GENOME_DIFF 1.0
#=TITLE Ara-3_1000gen_966A
#=AUTHOR Deatherage, Daniel
#=TIME 1000
#=POPULATION Ara-3
#=TREATMENT LTEE
#=CLONE A
#=MUTATOR_STATUS non-mutator
#=REFSEQ https://raw.githubusercontent.com/barricklab/LTEE/7da91974eafac0c5a8f903ae57275795d4395af2/reference/REL606.gbk
#=READSEQ ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR258/001/SRR2589001/SRR2589001_1.fastq.gz
#=READSEQ ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR258/001/SRR2589001/SRR2589001_2.fastq.gz
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2 changes: 0 additions & 2 deletions LTEE-clone-curated/Ara-3_1000gen_966B.gd
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#=GENOME_DIFF 1.0
#=TITLE Ara-3_1000gen_966B
#=AUTHOR Deatherage, Daniel
#=TIME 1000
#=POPULATION Ara-3
#=TREATMENT LTEE
#=CLONE B
#=MUTATOR_STATUS non-mutator
#=REFSEQ https://raw.githubusercontent.com/barricklab/LTEE/7da91974eafac0c5a8f903ae57275795d4395af2/reference/REL606.gbk
#=READSEQ ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR258/006/SRR2584856/SRR2584856_1.fastq.gz
#=READSEQ ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR258/006/SRR2584856/SRR2584856_2.fastq.gz
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74 changes: 35 additions & 39 deletions LTEE-clone-curated/Ara-3_15000gen_7179B.gd
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@@ -1,49 +1,45 @@
#=GENOME_DIFF 1.0
#=TITLE Ara-3_15000gen_7179B
#=AUTHOR Deatherage, Daniel
#=TIME 15000
#=POPULATION Ara-3
#=TREATMENT LTEE
#=CLONE B
#=MUTATOR_STATUS non-mutator
#=REFSEQ https://raw.githubusercontent.com/barricklab/LTEE/7da91974eafac0c5a8f903ae57275795d4395af2/reference/REL606.gbk
#=READSEQ ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR258/003/SRR2584863/SRR2584863_1.fastq.gz
#=READSEQ ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR258/003/SRR2584863/SRR2584863_2.fastq.gz
SNP 1 . REL606 9972 G
DEL 2 . REL606 16989 1 adjacent=IS150 within=3:2
MOB 3 . REL606 16989 IS150 1 4
SNP 4 . REL606 281923 T
INS 5 . REL606 433366 T repeat_length=1 repeat_new_copies=8 repeat_ref_copies=7 repeat_seq=T
INS 6 . REL606 473904 GC
MOB 7 . REL606 546191 IS1 1 9
SNP 8 . REL606 648692 T
DEL 9 . REL606 1270125 535 no_normalize=1
MOB 10 . REL606 1270660 IS150 -1 4
SNP 11 . REL606 1331794 A
MOB 12 . REL606 1462320 IS150 -1 3
SNP 13 . REL606 1733343 A
INS 14 . REL606 2103918 CCAGCCAGCCAGCCAGCCAGCCAG repeat_length=4 repeat_new_copies=13 repeat_ref_copies=7 repeat_seq=CCAG
MOB 15 . REL606 2122426 IS150 -1 3
INS 16 . REL606 2333539 T adjacent=ISRSO11
SNP 17 . REL606 2446984 C
SNP 18 . REL606 2665639 T
SNP 19 . REL606 2999330 A
MOB 20 . REL606 3015771 IS150 -1 3
MOB 21 . REL606 3268052 IS150 1 3
SNP 22 . REL606 3339313 C
SNP 23 . REL606 3401754 A
SNP 24 . REL606 3481820 G
SNP 25 . REL606 3488669 C
DEL 26 . REL606 3741966 177 mediated=IS1
DEL 27 . REL606 3895000 6460 mediated=IS150
SNP 28 . REL606 3909807 T
MOB 29 . REL606 4006278 IS150 1 -1 ins_start=CTT
SNP 30 . REL606 4100183 G
MOB 31 . REL606 4110237 IS150 -1 3
INS 32 . REL606 4110239 TG adjacent=IS150 within=31:1
SNP 33 . REL606 4201958 C
DEL 34 . REL606 4431394 2
MOB 35 . REL606 4613019 IS150 1 0 ins_start=TT
DEL 36 . REL606 4613020 1 adjacent=IS150 within=37:1
MOB 37 . REL606 4613020 IS150 1 3
SNP 38 . REL606 4616538 C
MOB 2 . REL606 16990 IS150 1 3
SNP 3 . REL606 281923 T
INS 4 . REL606 433366 T repeat_length=1 repeat_new_copies=8 repeat_ref_copies=7 repeat_seq=T
INS 5 . REL606 473904 GC
MOB 6 . REL606 546191 IS1 1 9
SNP 7 . REL606 648692 T
DEL 8 . REL606 1270125 535 no_normalize=1
MOB 9 . REL606 1270660 IS150 -1 4
SNP 10 . REL606 1331794 A
MOB 11 . REL606 1462320 IS150 -1 3
SNP 12 . REL606 1733343 A
INS 13 . REL606 2103918 CCAGCCAGCCAGCCAGCCAGCCAG repeat_length=4 repeat_new_copies=13 repeat_ref_copies=7 repeat_seq=CCAG
MOB 14 . REL606 2122426 IS150 -1 3
INS 15 . REL606 2333539 T adjacent=ISRSO11
SNP 16 . REL606 2446984 C
SNP 17 . REL606 2665639 T
SNP 18 . REL606 2999330 A
MOB 19 . REL606 3015771 IS150 -1 3
MOB 20 . REL606 3268052 IS150 1 3
SNP 21 . REL606 3339313 C
SNP 22 . REL606 3401754 A
SNP 23 . REL606 3481820 G
SNP 24 . REL606 3488669 C
DEL 25 . REL606 3741966 177 mediated=IS1
DEL 26 . REL606 3895000 6460 mediated=IS150
SNP 27 . REL606 3909807 T
MOB 28 . REL606 4006278 IS150 1 -1 ins_start=CTT
SNP 29 . REL606 4100183 G
MOB 30 . REL606 4110237 IS150 -1 3
INS 31 . REL606 4110239 TG adjacent=IS150 within=30:1
SNP 32 . REL606 4201958 C
DEL 33 . REL606 4431394 2
DEL 34 . REL606 4613020 1 adjacent=IS150 within=35:1
MOB 35 . REL606 4613020 IS150 1 3
SNP 36 . REL606 4616538 C
44 changes: 44 additions & 0 deletions LTEE-clone-curated/Ara-3_15000gen_ZDB445.gd
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#=GENOME_DIFF 1.0
#=TITLE Ara-3_15000gen_ZDB445
#=TIME 15000
#=POPULATION Ara-3
#=TREATMENT LTEE
#=CLONE X
#=REFSEQ https://raw.githubusercontent.com/barricklab/LTEE/7da91974eafac0c5a8f903ae57275795d4395af2/reference/REL606.gbk
#=READSEQ BarrickLab-Private:genomes/utexas_gsaf/Project_JA13577/EQ_1_CAGATC_L005_R1_001.fastq.gz
#=READSEQ BarrickLab-Private:genomes/utexas_gsaf/Project_JA13577/EQ_1_CAGATC_L005_R2_001.fastq.gz
SNP 1 . REL606 9972 G
MOB 2 . REL606 16990 IS150 1 3
SNP 3 . REL606 281923 T
INS 4 . REL606 433366 T repeat_length=1 repeat_new_copies=8 repeat_ref_copies=7 repeat_seq=T
INS 5 . REL606 473904 GC
MOB 6 . REL606 546191 IS1 1 9
SNP 7 . REL606 648692 T
SNP 8 . REL606 769968 C
DEL 9 . REL606 1270125 535 no_normalize=1
MOB 10 . REL606 1270660 IS150 -1 4
SNP 11 . REL606 1331794 A
MOB 12 . REL606 1462320 IS150 -1 3
SNP 13 . REL606 1733343 A
INS 14 . REL606 2103915 CAGCCAGCCAGCCAGCCAGCCAGC
MOB 15 . REL606 2122426 IS150 -1 3
INS 16 . REL606 2333539 T
SNP 17 . REL606 2446984 C
SNP 18 . REL606 2665639 T
SNP 19 . REL606 2999330 A
MOB 20 . REL606 3015771 IS150 -1 3
MOB 21 . REL606 3268052 IS150 1 3
SNP 22 . REL606 3339313 C
SNP 23 . REL606 3401754 A
SNP 24 . REL606 3481820 G
SNP 25 . REL606 3488669 C
DEL 26 . REL606 3741966 177 mediated=IS1
DEL 27 . REL606 3895000 6460 mediated=IS150
SNP 28 . REL606 3909807 T
SNP 29 . REL606 4100183 G
MOB 30 . REL606 4110237 IS150 -1 3
SNP 31 . REL606 4201958 C
DEL 32 . REL606 4431394 2
DEL 33 . REL606 4613020 1 adjacent=IS150 within=34:1
MOB 34 . REL606 4613020 IS150 1 3
SNP 35 . REL606 4616538 C
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