TB-Profiler result

Run: ERR4796852

Summary

Run ID: ERR4796852

Sample name:

Date: 01-04-2023 07:09:24

Number of reads: 5736973

Percentage reads mapped: 99.61

Strain: lineage3.1.2;lineage2.2.1.1

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 0.82
lineage2 East-Asian Beijing RD105 0.18
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.16
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.83
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.86
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.15
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.16
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 0.16 rifampicin
rpoB 761109 p.Asp435Asn missense_variant 0.14 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.2 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.18 isoniazid
embB 4247429 p.Met306Val missense_variant 0.19 ethambutol
ethA 4327292 p.Thr61Met missense_variant 0.17 ethionamide
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
mshA 575907 p.Ala187Val missense_variant 0.24
mshA 576108 p.Ala254Gly missense_variant 0.29
mshA 576113 p.Arg256Gly missense_variant 0.25
ccsA 620625 p.Ile245Met missense_variant 0.16
rpoB 759746 c.-61C>T upstream_gene_variant 0.75
rpoC 762434 c.-936T>G upstream_gene_variant 0.88
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.1
mmpS5 779615 c.-710C>G upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918104 c.165G>A synonymous_variant 0.76
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 0.86
PPE35 2170065 p.Ala183Gly missense_variant 0.23
Rv1979c 2221959 c.1206A>G synonymous_variant 0.12
Rv1979c 2222557 p.Thr203Ser missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.85
pncA 2289365 c.-125delC upstream_gene_variant 0.8
eis 2714846 p.Val163Ile missense_variant 0.2
ahpC 2726105 c.-88G>A upstream_gene_variant 0.79
pepQ 2860159 p.Ala87Gly missense_variant 0.23
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.58
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.24
alr 3841075 p.Pro116Ser missense_variant 0.8
rpoA 3878613 c.-106A>C upstream_gene_variant 0.22
embC 4240409 p.Pro183Ala missense_variant 0.21
embC 4242075 p.Arg738Gln missense_variant 0.83
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.2
embB 4246548 p.Pro12Gln missense_variant 0.22
embB 4246555 c.42G>C synonymous_variant 0.24
embB 4246556 p.Ala15Pro missense_variant 0.2
embB 4246563 p.Leu17Trp missense_variant 0.15
embB 4246567 c.54G>T synonymous_variant 0.21
embB 4247880 p.Val456Ala missense_variant 0.15
embB 4248115 c.1602C>T synonymous_variant 0.21
embB 4248324 p.Ala604Gly missense_variant 0.27
aftB 4267647 p.Asp397Gly missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0