Genbank

Other datasets deposited:

TnSeq of H37Rv in glycerol vs. cholesterol (Griffin et al, 2011)

no reads (PATRIC accession to come)

RNA-Seq of Rv3263/MamA deletion mutant (Scarlet Shell)

deposited in GEO: GSE52551, released on 11/21/2013

RNA-Seq of H37Rv in different conditions (Sarah Fortune)

deposited to GEO: GSE67035 - not released to public yet?

RNA-Seq of Rv2869/Rip1 and Rv3193c knock-outs

deposited to GEO on 4/8/15 - GSE67670, rel date: 10/1/18
Rv3193c used H37Rv as parental strain; Rip1 used Erdman
also selected in phenanthroline to chelate iron

TnSeq of Rv0050/PonA1 knock-out (Karen Kieser)

SRA: SRA277968
PATRIC: https://docs.patricbrc.org/news/2016/20160121-flute-experiment-2.html

TnSeq for H37Rv, Rv2680, Rv1432, Rv1565c in mice (d0 and d32) (Subbu, Run 69) - for NAR paper

for Genetic Interactions paper in NAR
deposited Aug 2016, hold till Sept 2017
Submission: SUB1906344, SUB1764800?
BioProject ID: PRJNA338716
BioSample accession: SAMN05570496, SRS1615326?
SRA accession num: SRP081827

TnSeq of H37Rv in vitro (14 replicates) for mBio paper

for Genetic Interactions paper in NAR
deposited Sept 2016, hold till Sept 2017
Submission: SUB1764800?, SUB1906344
BioProject ID: PRJNA341349
BioSample ID: SAMN05570496
SRA accession num: SRP083947

Mtb clinical isolates from Peru for CETR project

~1000 genomes deposited in GenBank
Fall 2016 (Yipin helped)
immediate release
example accession numbers:
- MMHU00000000 = 03-R0866
- MMHT00000000 = 97-05201
full list of accession numbers

PncA mutant library for Adam Yadon's paper

from runs 62, 68,70, and 74
fastq files deposited in SRA on 11/10/16
hold till 12/1/17
BioProject ID: PRJNA352866
SRA study accession: SRP093213

U19 TnSeq datasets deposited in SRA (March 2017):

final SRA accession: SRP101586 (hold to 4/1/18)
BioProject: PRJNA377978
SAMN06480744 Rv3916c Subu Run69 - 2 reps, in-vitro (d0 in mouse)
SAMN06480745 Rv0307c Subu Run69 - 2 reps, in-vitro (d0 in mouse)
SAMN06480746 Rv3717 Cara Run71 - 1 rep
SAMN06480747 Rv3594 Cara Run71 - 1 rep
SAMN06480748 Rv3811 Cara Run71 - 1 rep
SAMN06480749 Rv0950 Rebecca Run81 - 1 rep
SAMN06480750 Rv1096 Rebecca Run81 - 1 rep
SAMN06480751 Rv3684 Rebecca Run81 - 1 rep
SAMN06480752 Rv0954 Ruojun WCMC - 2 reps
SAMN06480753 Rv3671c Weizhen WCMC - 4 reps
GEO accession for RPKMs and DESeq2 results: GSE134574 (July 2019)

to do:

Ldt2? - Karen
MSMEG_0916 (Hesper, Run81)
Kasia - Run76: smeg KOs of blaR

aviumMD30 (MAH11; 32 contigs based on Illumina sequencing, Run75)

Bioproject: PRJNA380351
Biosample: SAMN06641776
Genbank: NBAW00000000 (32 contigs)
plamids: CM009838.1 (pMD1) and CM009839.1 (pMD2)
release date: 4/15/18
AGP files not needed for submission?

aviumMD36 (MAH11; genome completion as 1 contig using PacBio)

BioProject: PRJNA380351 (same as previously for aviumMD30)
BioSample: SAMN10878325
instrument: PacBio Sequel (650Mb long reads)
assembly method: BWA 0.7.12, Newbler 2.9, Blasr 5.3.2
release immediately (2/5/19)

Allison Carey's paper on TnSeq of Mtb clinical isolates

BioProject: PRJNA390291

WGS (genome sequences in Genbank): (release data: 2/23/18)

BioSample accn	strain	genome accn
SAMN07236903	581	NIXB00000000
SAMN07236904	621	NIXC00000000
SAMN07236905	630	NIXD00000000
SAMN07236906	631	NIXE00000000
SAMN07236907	632	NIXF00000000
SAMN07236908	641	NIXG00000000
SAMN07236909	662	NIXH00000000
SAMN07236910	663	NIXI00000000
SAMN07236911	667	NIXJ00000000

TnSeq fastq files deposited in SRA:

BioProject: PRJNA390291
study: SRP109851

release date: 7/13/18

SRA_accession	biosample_accession	library_ID
SRR5721632	SAMN07236904	621_1
SRR5721633	SAMN07236904	621_2
SRR5721630	SAMN07236905	630_1
SRR5721631	SAMN07236905	630_2
SRR5721636	SAMN07236906	631_1
SRR5721637	SAMN07236906	631_2
SRR5721634	SAMN07236907	632_1
SRR5721635	SAMN07236907	632_2
SRR5721638	SAMN07236908	641_1
SRR5721639	SAMN07236908	641_2
SRR5721623	SAMN07236909	662_1
SRR5721624	SAMN07236909	662_2
SRR5721621	SAMN07236910	663_1
SRR5721622	SAMN07236910	663_2
SRR5721627	SAMN07236911	667_1
SRR5721628	SAMN07236911	667_2
SRR5721625	SAMN07257464	Rv_1
SRR5721626	SAMN07257464	Rv_2
SRR5721629	SAMN07257464	Rv_3

SphA (NRPS) from Serratia marcescens

Emily Derbyshire (originally with John Clardy at Harvard, now at Duke)
Genbank accession number MF893109 (nucleotide sequence)
release date 9/25/17
used Sequin 15.50 on PC to make .sqn file; emailed to NCBI

WGS of BioAMS mutants for Dirk Schnappinger (9/26/17)

from Run55/analysis2 on HomeFrozen
based on version 'b', which was made from reads extracted from mapper files, since I don't have access to fastq files on megamouth
used dat2agp2.py to break genomes into contigs, but then uploaded .fsa files directly (via ftp) without running through Sequin
BioProject: PRJNA412260

release date: 10/1/18 (change to Apr 2018 for paper)

SUBID           BioProject      BioSample       Accession       Organism
---------------------------------------------------
SUB3078842      PRJNA412260     SAMN07703428    PDXL00000000    Mycobacterium tuberculosis BioAMS25R1
SUB3078842      PRJNA412260     SAMN07703427    PDXM00000000    Mycobacterium tuberculosis BioAMS20R1
SUB3078842      PRJNA412260     SAMN07703426    PDXN00000000    Mycobacterium tuberculosis BioAMS10R1
SUB3078842      PRJNA412260     SAMN07703425    PDXO00000000    Mycobacterium tuberculosis BioAMS5R1
SUB3078842      PRJNA412260     SAMN07703424    PDXP00000000    Mycobacterium tuberculosis BioAMSR

WGS of Sanofi-8918 mutants for Carl Nathan and Elaine Ballinger (12/19/17)

from Run75 and Run65
used dat2agp2.py to break genomes into contigs, but then uploaded .fsa files directly (via ftp) without running through Sequin
BioSample SUB3358216, release 1/1/19
- note: initially, it looks like I didn't associate it with the BioProject id, it was set for immediate release
- 8918-A1, SAMN08205014, PKPX0000000
- 8918-A4, SAMN08205015, PKPW0000000
- 8918-A6, SAMN08205016, PKPV0000000
- 8918-B1, SAMN08205017, PKPU0000000
- 8918-B2, SAMN08205018, PKPT0000000
- 8981-B3, SAMN08205019, PKPS0000000
- 8918-B4, SAMN08205020, PKPR0000000
- 8918-B5, SAMN08205021, PKPQ0000000
BioProject, SUB3358077, PRJNA423087, release 1/1/19, funding source: U19 AI111143 (TBRU, Carl)
WGS: SUB3358332

Weizhen Xu's TnSeq data of H37Rv in various antibiotics

submitted reads to SRA (3/1/18) immediate release
published: Xu et al (2017), AAC.
submission file in Projects/TnSeq/Weizhen/ folder
BioProject: PRJNA436485

SRA accession: SRP133737

  STUDY: PRJNA436485 (SRP133737)
  SAMPLE: Vancomycin_rep1_16 (SRS3009535)
  EXPERIMENT: 26 (SRX3753421)
  RUN: WTV1_16b.fastq.gz (SRR6794428)

MAV clinical isolates for Nisha Kannan and Magnus Steigedal

BioProject: PRJNA447977
SRA accession: SRP136774
deposited reads (.fastq files) in SRA on 3/29/18, release on 3/29/19, changed to 4/4/18

did not deposit genome sequences

  4.1 MAV25
  4.2 MAV30
  4.3 MAV41
  4.4 MAV14
  4.5 MAV15
  4.6 MAV12
  9.1 MAV03
  9.2 MAV40
  9.3 MAV26 - Run85
  9.4 MAV33
  9.5 MAV20
  9.6 MAV01 - Run61
  13.1 MAV6
  13.2 MAV39
  13.3 MAV28
  13.4 MAV02

U19 TnSeq datasets

deposited in Mar 2018 (in prep for annual NIH meeting)
includes datasets for Rv0950,Rv1096,Rv3684(Run81,Hesper)
reads sent to SRA; interactions (from resampling) sent to PATRIC

TnSeq of LDT knockouts in M. smeg for Kasia Baranowski (Rubin lab)

BioProject: PRJNA451029 (TnSeq of L,D-transpeptidase knockouts in Mycobacterium smegmatis)
SRA accession: SRP141343
deposited reads (.fastq files) in SRA on 4/20/18, immediate release

Run94

  5761 TnSeq_KB303 deltaAEBCGF
  5762 TnSeq_KB241 deltaAEBCG
  5763 TnSeq_KB214 deltaAEBF
  5764 TnSeq_KB215 deltaAEBC
  5765 TnSeq_KB207 deltaAEB
  5766 TnSeq_KB85 WT

added the NADA samples from Run71 (4/27/18)
added the WGS samples from Run94 (6/21/18) - deltaLdtAEBCGF, Msmeg-KB

TnSeq of ESX-1 knockouts for U19 in SRA (8/2/18)

Rebecaa Audette (Rubin lab); Run96
TnSeq_KO_eccD1, TnSeq_KO_espI, TnSeq_KO_PE35, TnSeq_KO_PPE68
BioProject: PRJNA484233 (8/2/18)
SRA accession: SRP156233, traces

RNAseq data for U19 knockouts

Shoko's samples on Run107
3 replicates each of H37Rv, Rv0307c, Rv0950c, Rv1096, Rv1432, Rv1565c, Rv2680, Rv3484, Rv3684, Rv3916c
12/27/18 - deposited in SRA (will do GEO later)
BioProject: PRJNA511742
release data: 1/1/20
BioSample accession numbers: SAMN10654087-116

RNA-seq for M. smegmatis LepA knock-out

Skye Fishbein (Rubin lab)
BioProject: PRJNA518044
SRA Study: SRP183056
GEO: GSE126130 (gene counts and DeSeq analysis: smeg_LepA_RNAseq_counts.dat, lepA_DeSeq_KO_vs_Wt.txt)

release date: 2/1/20

accession	sample_name	isolate
SAMN10852567	Skye-177-1	WT
SAMN10852568	Skye-177-2	WT
SAMN10852569	Skye-177-3	WT
SAMN10852570	Skye-178-4	LepA-compl
SAMN10852571	Skye-178-5	LepA-compl
SAMN10852572	Skye-178-6	LepA-compl
SAMN10852573	Skye-181-7	LepA-KO
SAMN10852574	Skye-181-8	LepA-KO
SAMN10852575	Skye-181-9	LepA-KO

link to my seqs on Genbank

re-run mapper on final seq; run dat2agp.py
WGS submission
NCBI instructions on how to submit
validate .agp file
web form to make template (.sbt) file
create .sqn file using tbl2asn (command-line)
(Sequin - not needed!)
Note: must use .fsa for sequence file ***
on my PC, see C:\Temp\Sequencing\Sequin\
Submit

> cd C:\Temp\sequencing\Sequin\H37RvCO
> ..\tbl2asn -t template.sbt -p C:\Temp\sequencing\Sequin\H37RvCO -V v -a s

project id strain name accession number internal version coverage contigs notes
47937 Mycobacterium tuberculosis H37RvCO AJSF00000000 H37RvCO4 79.2x 125 Colorado State (Karen Dobos)
47933 Mycobacterium tuberculosis H37RvAE H37RvAE4 57.7x 12
47935 Mycobacterium tuberculosis H37RvMA H37RvMA2 62.3x 112*
47941 Mycobacterium tuberculosis H37RvLP H37RvLPb 151.3x 88*
47943 Mycobacterium tuberculosis H37RvJO H37RvJO2 163.3x
47939 Mycobacterium tuberculosis H37RvHA H37RvHA 29.4x previously H37RvSF4
39761 Mycobacterium tuberculosis KZN_4207 NZ_ACVS00000000.2 KZN_4207tam 134x 59 drug-sensitive
39765 Mycobacterium tuberculosis KZN V2475 NZ_ACVT00000000.2 V2475b 175x 84 MDR
39767 Mycobacterium tuberculosis KZN R506 NZ_ACVU00000000.2 R506b 188x 74 XDR
46665 Mycobacterium tuberculosis HN878 ADNF01000000 HN878d
46667 Mycobacterium tuberculosis X122 ADNG01000000 X122g
46669 Mycobacterium tuberculosis R1207 ADNH01000000 R1207g
72237 Mycobacterium thermoresistibile ATCC 19527 AGVE00000000.1 thermov10 153x 56 KEK_08252011 (annotation)

Panama strains

Notes:

no merging of contigs, min gap length of 10
This is a circular chromosome. There is no gap between the first and last contigs. They are broken into 2 separate contigs since M. tuberculosis genomes start with the first nucleotide of DnaA by convention.
Fedora Lanzas, Instituto Conmemorativo Gorgas de Estudios de la Salud, ICGES, Panama

Steps:

prepare .agp and .fsa files (using dat2agp.py and post-processing)
create BioProject (just click on previous Submmission and create a copy and change strain id under Target)
create template (copy and change Bioproject id)
run tbl2asn to create .sqn file
create WholeGenomeSubmission (give BioProject id with PRJNA)
upload .sqn and .agp files
"fixed" means I add the additinonal fields in tbl2asn shown below and re-uploaded the .sqn file

> cd C:\tom\fedora\genbank
> tbl2asn -t template-PanR0601.sbt -i PanR0601.fsa -V v -a s -j "[collection-date=2006] [isolation-source=clinical isolate] [country=Panama] [host=Homo sapiens] [note=multi-drug resistant]"
(new version of tbl2asn in fedora\genbank directory)
(copy template.sbt and update BioProject id)

representative	cluster	source sequence	cov	contigs	Submission	BioProject	locus tag	date	accession
PanR0802	c1	fedora0802c_IS.fna	72.0x	79	SUB142201	PRJNA182111	F508	11/23/12	ANZH00000000
PanR0201	c2	fedora0201c_IS.fna	68.0x	97	SUB140329	PRJNA182109	F507	11/23/12	ANZG00000000
PanR0704	c3	fedora0704i_IS.fna	85.1x	67	SUB140327	PRJNA181126	F379	11/16/12	ANNN00000000
PanR1005	c4	fedora1005_IS.fna	73.0x	87	SUB142203	PRJNA182112	F509	11/23/12	ANZI000000000
PanR0202		fedora0202c_IS.fna	90.2x	57	SUB258631	PRJNA206559	M208	6/4/13	ATAS00000000
PanR0203		fedora0203c_IS.fna	80.7x	110	SUB263721	PRJNA207751	M389	6/9/13	ATML00000000
PanR0205		fedora0205e_IS.fna	75.1x	131	SUB263722	PRJNA207752	M390	6/9/13	ATMM00000000
PanR0206		fedora0206b_IS.fna	134.3x	71	SUB263723	PRJNA207753	M391	6/9/13	ATMN00000000
PanR0207		fedora0207g_IS.fna	144.3x	74	SUB263724	PRJNA207754	M392	6/9/13	ATMQ00000000
PanR0208		fedora0208e_IS.fna	69.0x	157	SUB263725	PRJNA207755	M393	6/9/13	ATMO00000000
PanR0209		fedora0209_IS.fna	59.1x	53	SUB263726	PRJNA207756	M394	6/9/13	ATMP00000000
PanR0301		fedora0301c_IS.fna	85.1x	146	SUB274134	PRJNA208573	M535	6/15/13	ATET00000000
PanR0304		fedora0304b_IS.fna	43.4x	217	SUB274135	PRJNA208574	M536	6/15/13	ATES00000000
PanR0305		fedora0305_IS.fna	45.6x	115	SUB274136	PRJNA208575	M537	6/15/13	ATER00000000
PanR0306		fedora0306b_IS.fna	49.1x	186	SUB274137	PRJNA208576	M538	6/15/13	ATEQ00000000
PanR0307		fedora0307c_IS.fna	111.3x	153	SUB274138	PRJNA208577	M539	6/15/13	ATEP00000000
PanR0308		fedora0308g_IS.fna	130.4x	85	SUB274139	PRJNA208578	M540	6/15/13	ATEO00000000
PanR0309		fedora0309c_IS.fna	145.9x	43	SUB274140	PRJNA208579	M541	6/15/13	ATEN00000000
PanR0311		fedora0311b_IS.fna	35.2x	241	SUB274141	PRJNA208580	M542	6/15/13	ATEM00000000
PanR0313		fedora0313c_IS.fna	77.5x	49	SUB274142	PRJNA208581	M543	6/15/13	ATEL00000000
PanR0314		fedora0314e_IS.fna	80.6x	76	SUB274143	PRJNA208582	M544	6/15/13	ATEK00000000
PanR0315		fedora0315_IS.fna	42.4x	237	SUB274144	PRJNA208583	M545	6/15/13	ATEJ00000000
PanR0316		fedora0316c_IS.fna	76.0x	110	SUB274145	PRJNA208584	M546	6/15/13	ATEI00000000
PanR0317		fedora0317b_IS.fna	26.8x	309	SUB274146	PRJNA208585	M547	6/15/13	ATEH00000000
PanR0401		fedora0401b_IS.fna	44.2x	237	SUB274257	PRJNA208595	M549	6/16/13	ATEG00000000
PanR0402		fedora0402_IS.fna	63.5x	129	SUB274258	PRJNA208596	M550	6/16/13	ATEF00000000
PanR0403		fedora0403_IS.fna	68.2x	131	SUB274259	PRJNA208597	M551	6/16/13	ATEE00000000
PanR0404		fedora0404_IS.fna	70.5x	134	SUB274260	PRJNA208598	M552	6/16/13	ATED00000000
PanR0405		fedora0405c_IS.fna	139.7x	73	SUB274261	PRJNA208599	M553	6/16/13	ATEC00000000
PanR0407		fedora0407b_IS.fna	37.2x	487	SUB274262	PRJNA208600	M554	6/16/13	ATEB00000000
PanR0408		fedora0408b_IS.fna	45.3x	352	SUB274263	PRJNA208601	M555	6/16/13
PanR0409		fedora0409_IS.fna	69.0x	102	SUB274264	PRJNA208602	M556	6/16/13	ATEA00000000
PanR0410		fedora0410_IS.fna	67.3x	69	SUB274265	PRJNA208603	M557	6/16/13	ATDZ00000000
PanR0411		fedora0411_IS.fna	72.5x	71	SUB274266	PRJNA208604	M558	6/16/13	ATDY00000000
PanR0412		fedora0412_IS.fna	46.7x	88	SUB274267	PRJNA208605	M559	6/16/13	ATDX00000000
PanR0501		fedora0501_IS.fna	74x	122	SUB283445	PRJNA210047	M839	6/30/13	ATRP00000000
PanR0503		fedora0503_IS.fna	29x	142	SUB283446	PRJNA210048	M840	6/30/13	ATRQ00000000
PanR0505		fedora0505_IS.fna	69x	139	SUB283447	PRJNA210049	M841	6/30/13	ATRR00000000
PanR0601		fedora0601c_IS.fna	38x	669(!)	SUB283458	PRJNA210050	M842	6/30/13	ATRS00000000
PanR0602		fedora0602_IS.fna	73x	102	SUB283459	PRJNA210051	M843	6/30/13	ATRT00000000
PanR0603		fedora0603_IS.fna	56x	150	SUB283460	PRJNA210052	M844	6/30/13	ATRU00000000
PanR0604		fedora0604_IS.fna	23x	134	SUB283461	PRJNA210053	M845	6/30/13	ATRV00000000
PanR0605		fedora0605_IS.fna	67x	84	SUB283462	PRJNA210054	M846	6/30/13	ATRW00000000
PanR0606		fedora0606c_IS.fna	79x	59	SUB283463	PRJNA210055	M847	6/30/13	ATRX00000000
PanR0607		fedora0607c_IS.fna	118x	81	SUB283464	PRJNA210056	M848	6/30/13	ATRY00000000
PanR0609		fedora0609c_IS.fna	102x	77	SUB283465	PRJNA210057	M849	6/30/13	ATRZ00000000
PanR0610		fedora0610c_IS.fna	79x	96	SUB283466	PRJNA210058	M850	6/30/13	ATSA00000000
PanR0611		fedora0611c_IS.fna	87x	146	SUB283467	PRJNA210059	M851	6/30/13	ATSB00000000
PanR0702		fedora0702f_IS.fna	58x	148	SUB283476	PRJNA210060	M852	6/30/13	ATSC00000000
PanR0703		fedora0703c_IS.fna	70x	155	SUB283477	PRJNA210061	M853	6/30/13	ATSD00000000
PanR0707		fedora0707_IS.fna	90x	143	SUB283478	PRJNA210062	M854	6/30/13	ATSE00000000
PanR0708		fedora0708c_IS.fna	75x	55	SUB283479	PRJNA210063	M855	6/30/13	ATSF00000000
PanR0801		fedora0801c_IS.fna	73x	117	SUB283480	PRJNA210064	M856	6/30/13	ATSG00000000
PanR0803		fedora0803c_IS.fna	116x	53	SUB283481	PRJNA210065	857M	6/30/13	ATSH00000000
PanR0804		fedora0804_IS.fna	104x	145	SUB283482	PRJNA210066	M858	6/30/13	ATSI00000000
PanR0805		fedora0805b_IS.fna	39x	281	SUB283483	PRJNA210067	M859	6/30/13	ATSJ00000000
PanR0902		fedora0902c_IS.fna	49x	170	SUB283495	PRJNA210068	M860	6/30/13	ATSK00000000
PanR0903		fedora0903_IS.fna	98x	68	SUB283496	PRJNA210069	M861	6/30/13	ATSL00000000
PanR0904		fedora0904_IS.fna	107x	84	SUB283497	PRJNA210070	M862	6/30/13	ATSM00000000
PanR0906		fedora0906c_IS.fna	101x	44	SUB283498	PRJNA210071	M863	6/30/13	ATSN00000000
PanR0907		fedora0907c_IS.fna	84x	84	SUB283499	PRJNA210072	M864	6/30/13	ATSO00000000
PanR0908		fedora0908c_IS.fna	45x	144	SUB283500	PRJNA210073	M865	6/30/13	ATSP00000000
PanR0909		fedora0909_IS.fna	136x	144	SUB283501	PRJNA210074	M866	6/30/13	ATSQ00000000
PanR1006		fedora1006_IS.fna	64x	114	SUB283506	PRJNA210075	M867	6/30/13	ATST00000000
PanR1007		fedora1007_IS.fna	98x	54	SUB283502	PRJNA210076	M868	6/30/13	ATSR00000000
PanR1101		fedora1101e_IS.fna	76x	140	SUB283503	PRJNA210077	M869	6/30/13	ATSS00000000

Here the accession numbers for the H37Rv strains:

SUBID           BioProject      Accession       Organism
---------------------------------------------------
SUB048510       PRJNA47937      AJSF00000000    Mycobacterium tuberculosis H37RvCO

PRJNA47933 Mycobacterium tuberculosis H37RvAE
PRJNA47935 Mycobacterium tuberculosis H37RvMA
PRJNA47937 Mycobacterium tuberculosis H37RvCO
PRJNA47939 Mycobacterium tuberculosis H37RvHA
PRJNA47941 Mycobacterium tuberculosis H37RvLP
PRJNA47943 Mycobacterium tuberculosis H37RvJO

KZN strains...

project_id    organism  name                          accession
--------------------------------------------------------------------
PID: 39761    Mycobacterium tuberculosis KZN 4207     ACVS00000000
PID: 39765    Mycobacterium tuberculosis KZN V2475    ACVT00000000
PID: 39767    Mycobacterium tuberculosis KZN R506     ACVU00000000

Beijing strains...

PID     Organism                          accession    version
-------------------------------------------------------------------
46665   Mycobacterium tuberculosis HN878  ADNF00000000 ADNF01000000
46667   Mycobacterium tuberculosis X122   ADNG00000000 ADNG01000000
46669   Mycobacterium tuberculosis R1207  ADNH00000000 ADNH01000000

M. thermo...

PID     Organism                                        Accession
--------------------------------------------------------------------
72237   Mycobacterium thermoresistibile ATCC 19527      AGVE00000000

project id	strain name	accession number	internal version	coverage	contigs	notes
47937	Mycobacterium tuberculosis H37RvCO	AJSF00000000	H37RvCO4	79.2x	125	Colorado State (Karen Dobos)
47933	Mycobacterium tuberculosis H37RvAE		H37RvAE4	57.7x	12
47935	Mycobacterium tuberculosis H37RvMA		H37RvMA2	62.3x	112*
47941	Mycobacterium tuberculosis H37RvLP		H37RvLPb	151.3x	88*
47943	Mycobacterium tuberculosis H37RvJO		H37RvJO2	163.3x
47939	Mycobacterium tuberculosis H37RvHA		H37RvHA	29.4x		previously H37RvSF4
39761	Mycobacterium tuberculosis KZN_4207	NZ_ACVS00000000.2	KZN_4207tam	134x	59	drug-sensitive
39765	Mycobacterium tuberculosis KZN V2475	NZ_ACVT00000000.2	V2475b	175x	84	MDR
39767	Mycobacterium tuberculosis KZN R506	NZ_ACVU00000000.2	R506b	188x	74	XDR
46665	Mycobacterium tuberculosis HN878	ADNF01000000	HN878d
46667	Mycobacterium tuberculosis X122	ADNG01000000	X122g
46669	Mycobacterium tuberculosis R1207	ADNH01000000	R1207g
72237	Mycobacterium thermoresistibile ATCC 19527	AGVE00000000.1	thermov10	153x	56	KEK_08252011 (annotation)