TB-Profiler result

Run: ERR3077948

Summary

Run ID: ERR3077948

Sample name:

Date: 01-04-2023 00:12:21

Number of reads: 1949837

Percentage reads mapped: 99.4

Strain: lineage3.1.1;lineage1.1.2

Drug-resistance: MDR-TB


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.38
lineage1 Indo-Oceanic EAI RD239 0.6
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.59
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.27
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.61
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.39
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
rpoB 761139 p.His445Asp missense_variant 0.28 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.72 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.62 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289105 p.Ala46Val missense_variant 0.69 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.6 ethambutol
embB 4247729 p.Gly406Ser missense_variant 0.34 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 0.38 ethambutol
gid 4408087 c.115delC frameshift_variant 0.29 streptomycin
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrB 6112 p.Met291Ile missense_variant 0.59
gyrB 6124 c.885C>T synonymous_variant 0.55
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.55
gyrA 9143 c.1842T>C synonymous_variant 0.62
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 0.42
rpoC 762434 c.-936T>G upstream_gene_variant 0.35
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.55
rpoC 763886 c.517C>A synonymous_variant 0.59
rpoC 764585 p.Leu406Phe missense_variant 0.24
rpoC 765171 p.Pro601Leu missense_variant 0.51
rpoC 766488 p.Pro1040Arg missense_variant 0.64
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.66
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918004 p.Gln22Arg missense_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.71
PPE35 2168435 c.2178C>T synonymous_variant 0.59
PPE35 2170461 p.Gly51Glu missense_variant 0.38
Rv1979c 2222308 p.Asp286Gly missense_variant 0.62
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.32
pncA 2289365 c.-125delC upstream_gene_variant 0.31
pncA 2289472 c.-231G>A upstream_gene_variant 0.65
kasA 2518132 c.18C>T synonymous_variant 0.58
ahpC 2726051 c.-142G>A upstream_gene_variant 0.62
ahpC 2726105 c.-88G>A upstream_gene_variant 0.33
Rv2752c 3064632 c.1560C>T synonymous_variant 0.67
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339741 c.624G>A synonymous_variant 0.58
Rv3083 3448714 p.Asp71His missense_variant 0.67
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.61
fprA 3474700 p.Gly232Ser missense_variant 0.68
fprA 3475159 p.Asn385Asp missense_variant 0.51
clpC1 4040517 p.Val63Ala missense_variant 0.66
embC 4240172 p.Val104Met missense_variant 0.42
embC 4240671 p.Thr270Ile missense_variant 0.67
embC 4240756 c.894G>T synonymous_variant 0.64
embC 4241042 p.Asn394Asp missense_variant 0.64
embC 4241562 p.Arg567His missense_variant 0.39
embC 4242075 p.Arg738Gln missense_variant 0.37
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.68
embA 4245969 p.Pro913Ser missense_variant 0.62
embB 4247646 p.Glu378Ala missense_variant 0.71
embB 4249673 p.Ser1054Pro missense_variant 0.62
ubiA 4269387 p.Glu149Asp missense_variant 0.46
aftB 4269606 c.-770T>C upstream_gene_variant 0.58
ethA 4326453 p.Ala341Thr missense_variant 0.65
ethA 4328209 c.-736C>A upstream_gene_variant 0.71
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.63
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.54
gid 4407935 p.Leu90Val missense_variant 0.72
gid 4407944 p.Gln87Glu missense_variant 0.69