TB-Profiler result

Run: ERR3077950
Summary

Run ID: ERR3077950

Sample name:

Date: 01-04-2023 00:12:16

Number of reads: 649798

Percentage reads mapped: 99.45

Strain: lineage3.1.1

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 0.98
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili RD750 1.0
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 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247729 p.Gly406Ser missense_variant 1.0 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 0.94 ethambutol
gid 4408087 c.115delC frameshift_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
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 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762974 p.Gln1056His missense_variant 0.28
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764585 p.Leu406Phe missense_variant 0.67
rpoC 765568 p.Met733Ile missense_variant 0.11
rpoC 765597 p.Lys743Arg missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776996 c.1485C>A synonymous_variant 0.11
mmpL5 777263 c.1218G>A synonymous_variant 0.29
mmpR5 779113 p.Trp42Arg missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302967 p.Pro13Thr missense_variant 0.11
fbiC 1302971 p.Ser14Asn missense_variant 0.11
fbiC 1305169 p.Gln747Glu missense_variant 0.12
fbiC 1305316 p.Thr796Ala missense_variant 0.22
Rv1258c 1407187 p.Met52Val missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475259 n.1602T>G non_coding_transcript_exon_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170082 c.531T>G synonymous_variant 0.15
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2289624 c.-383A>C upstream_gene_variant 0.11
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2860024 p.Arg132Pro missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840430 p.Asn331Tyr missense_variant 0.11
clpC1 4038921 p.Phe595Ser missense_variant 0.11
clpC1 4039471 p.Ile412Val missense_variant 0.25
clpC1 4039484 c.1221T>G synonymous_variant 0.25
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246746 p.Asp78Gly missense_variant 0.25
whiB6 4338596 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0