TB-Profiler result

Run: SRR6832231
Summary

Run ID: SRR6832231

Sample name:

Date: 04-04-2023 17:18:32

Number of reads: 581050

Percentage reads mapped: 99.6

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 0.96
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.Ser450Phe missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247429 p.Met306Val 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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9386 c.2085T>C synonymous_variant 0.1
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491758 p.Ser326Pro missense_variant 0.2
mshA 575818 c.472delT frameshift_variant 0.12
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.5
rpoB 760989 p.Arg395Trp missense_variant 0.2
rpoB 761461 p.Arg552His missense_variant 0.2
rpoB 761513 c.1707G>A synonymous_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763267 p.Ala1154Val missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775734 p.Phe916Ser missense_variant 0.17
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 778970 c.-65A>G upstream_gene_variant 0.4
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475953 n.2296A>G non_coding_transcript_exon_variant 0.5
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834798 c.1257C>T synonymous_variant 0.13
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 2168280 p.Pro778Leu missense_variant 0.25
PPE35 2169010 p.Pro535Thr missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288820 p.Gln141Leu missense_variant 0.18
kasA 2518513 c.399C>A synonymous_variant 0.22
kasA 2518761 p.Met216Arg missense_variant 0.29
Rv2752c 3064574 p.Trp540Gly missense_variant 1.0
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086777 c.-43A>T upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449425 c.924_925delGC frameshift_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612207 p.Thr304Ala missense_variant 0.5
Rv3236c 3612224 p.Ala298Val missense_variant 0.4
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244396 c.1164T>C synonymous_variant 0.29
embB 4247537 p.His342Tyr missense_variant 0.22
aftB 4267177 p.Ile554Phe missense_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267799 c.1038G>A synonymous_variant 0.5
whiB6 4338371 p.Thr51Pro missense_variant 1.0
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