TB-Profiler result

Run: ERR5866470
Summary

Run ID: ERR5866470

Sample name:

Date: 02-04-2023 00:42:13

Number of reads: 456917

Percentage reads mapped: 99.13

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473247 n.1402C>T non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol
ethA 4326166 c.1307dupC frameshift_variant 1.0 ethionamide, 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 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761985 p.Asp727Tyr missense_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764916 p.Leu516Pro missense_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 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304053 p.Asp375Tyr missense_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473458 n.-200G>T upstream_gene_variant 0.29
rrl 1476693 n.3036G>T non_coding_transcript_exon_variant 0.17
rpsA 1833350 c.-192G>T upstream_gene_variant 0.17
rpsA 1833853 p.Lys104Asn missense_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834420 c.879C>A synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918000 p.Gln21Lys missense_variant 0.2
tlyA 1918413 c.474C>A synonymous_variant 0.12
tlyA 1918434 c.495C>A synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169942 p.Leu224Pro missense_variant 0.1
Rv1979c 2222815 p.Leu117Gln missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290123 c.-882G>T upstream_gene_variant 0.2
kasA 2518875 p.Ala254Asp missense_variant 0.12
folC 2747647 c.-49T>C upstream_gene_variant 0.33
Rv2752c 3065451 p.Gln247His missense_variant 0.12
thyX 3067417 c.528delC frameshift_variant 0.2
thyA 3074400 c.72C>A synonymous_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613251 c.-135C>T upstream_gene_variant 0.22
fbiA 3641271 p.Tyr243* stop_gained 0.13
alr 3841539 c.-119C>A upstream_gene_variant 0.17
rpoA 3877573 p.Pro312Gln missense_variant 0.15
clpC1 4038305 c.2400C>A synonymous_variant 0.14
clpC1 4039302 p.Trp468Leu missense_variant 0.25
panD 4044158 p.Glu42* stop_gained 0.15
embC 4240084 c.222G>T synonymous_variant 0.17
embC 4241982 p.Pro707Gln missense_variant 0.14
embC 4242074 p.Arg738Trp missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4245944 c.-570C>A upstream_gene_variant 0.14
embB 4249132 c.2619G>T synonymous_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4327467 p.Glu3* stop_gained 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0