TB-Profiler result

Run: ERR2514729

Summary

Run ID: ERR2514729

Sample name:

Date: 31-03-2023 20:31:33

Number of reads: 604094

Percentage reads mapped: 99.28

Strain: lineage3

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 0.99
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 761095 p.Leu430Pro missense_variant 1.0 rifampicin
rpoB 761108 p.Met434Ile missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.95 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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 6763 c.-539G>A upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9461 c.2160C>T synonymous_variant 0.14
gyrA 9629 c.2328C>T synonymous_variant 1.0
fgd1 490622 c.-161G>T upstream_gene_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619995 c.107delT frameshift_variant 0.17
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765706 c.2337G>A synonymous_variant 0.12
rpoC 765732 p.Ala788Glu missense_variant 0.14
rpoC 766490 p.Arg1041Gly missense_variant 0.16
rpoC 766582 c.3213C>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777147 p.Pro445His missense_variant 0.12
mmpL5 777157 p.Arg442Trp missense_variant 0.13
mmpL5 778624 c.-144C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406696 c.645G>T synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674742 p.Lys181Glu missense_variant 0.14
inhA 1674858 c.657G>A synonymous_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102605 c.438G>A synonymous_variant 0.14
katG 2154120 p.Met664Ile missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156096 p.Pro6Ser missense_variant 0.12
PPE35 2167707 p.Gly969Asp missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 0.96
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
eis 2715347 c.-15C>T upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746653 p.Gly316Ser missense_variant 0.12
Rv2752c 3064698 c.1494C>G synonymous_variant 0.13
Rv2752c 3065069 p.His375Tyr missense_variant 1.0
Rv2752c 3065224 p.His323Leu missense_variant 0.12
Rv2752c 3067080 c.-890_-889delTGinsCC upstream_gene_variant 0.12
thyX 3067922 c.24C>T synonymous_variant 0.14
thyA 3074298 p.Glu58Asp missense_variant 0.13
thyA 3074578 c.-107C>T upstream_gene_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087837 p.Ala340Thr missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>T synonymous_variant 0.11
whiB7 3568702 c.-23C>A upstream_gene_variant 1.0
fbiB 3641517 c.-18C>T upstream_gene_variant 0.12
alr 3840937 c.484C>T synonymous_variant 0.12
alr 3841473 c.-53G>A upstream_gene_variant 1.0
embC 4240388 p.Asn176His missense_variant 1.0
embC 4241175 p.Ser438Tyr missense_variant 0.12
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242706 p.Asp948Glu missense_variant 0.12
embC 4242776 p.Gln972Lys missense_variant 0.12
aftB 4268114 c.723G>T synonymous_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408012 c.190dupC frameshift_variant 0.93