TB-Profiler result

Run: ERR4828358

Summary

Run ID: ERR4828358

Sample name:

Date: 01-04-2023 18:49:56

Number of reads: 925401

Percentage reads mapped: 99.47

Strain: lineage2.2.1

Drug-resistance: HR-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
katG 2156062 p.Ser17Asn missense_variant 0.12 isoniazid
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
gyrB 6182 p.Thr315Ser missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8124 p.Pro275Ser missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9493 p.Tyr731Cys missense_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.35
ccsA 620348 p.Gly153Glu missense_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761035 p.Thr410Arg missense_variant 0.14
rpoB 763029 p.Ala1075Thr missense_variant 0.14
rpoB 763252 p.Leu1149Gln missense_variant 0.12
rpoC 764705 c.1336C>T synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776608 p.Gln625* stop_gained 0.13
mmpL5 777818 c.663G>C synonymous_variant 0.1
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781615 p.Val19Ala missense_variant 0.11
fbiC 1303615 p.Ala229Thr missense_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473165 n.1320C>T non_coding_transcript_exon_variant 0.4
rpsA 1834151 p.Asn204Tyr missense_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834199 p.Val220Ile missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154205 p.Ala636Val missense_variant 0.12
katG 2154330 c.1782C>T synonymous_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155318 p.Leu265Pro missense_variant 0.12
PPE35 2167866 p.Leu916Pro missense_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168462 c.2151C>T synonymous_variant 0.14
PPE35 2168494 p.Gly707Ser missense_variant 0.22
PPE35 2168873 p.Asn580Lys missense_variant 0.67
Rv1979c 2222318 p.Ala283Thr missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289577 c.-336A>G upstream_gene_variant 0.18
kasA 2519178 p.Ser355* stop_gained 0.14
folC 2746811 p.Phe263Ser missense_variant 0.1
pepQ 2860353 p.Met22Ile missense_variant 0.12
pepQ 2860426 c.-8C>T upstream_gene_variant 0.18
Rv2752c 3065291 p.Val301Met missense_variant 0.17
Rv2752c 3065417 p.Val259Leu missense_variant 0.15
Rv2752c 3065706 c.486G>A synonymous_variant 0.18
Rv2752c 3065859 c.333G>A synonymous_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086897 c.78A>G synonymous_variant 0.18
ald 3087761 c.942C>A synonymous_variant 0.17
Rv3083 3448589 p.Asp29Val missense_variant 0.17
Rv3083 3449145 c.642G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475216 p.Asp404Asn missense_variant 0.13
Rv3236c 3612192 p.Gly309Arg missense_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613100 c.16delG frameshift_variant 0.17
fbiB 3641028 c.-507A>G upstream_gene_variant 0.12
alr 3840441 c.979delG frameshift_variant 0.18
alr 3841356 p.Ser22Leu missense_variant 0.11
alr 3841440 c.-20A>T upstream_gene_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243311 p.Leu27Val missense_variant 0.1
embA 4243460 c.228C>T synonymous_variant 0.96
embA 4244836 p.Leu535Pro missense_variant 0.11
embA 4246434 p.Gln1068* stop_gained 0.25
embB 4248251 p.Gly580Cys missense_variant 0.33
aftB 4267206 p.Val544Glu missense_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267836 p.Met334Thr missense_variant 0.2
ubiA 4269250 p.Glu195Ala missense_variant 0.15
aftB 4269489 c.-653C>T upstream_gene_variant 0.12
ethA 4326676 p.Ser266Arg missense_variant 1.0
whiB6 4338216 p.Asn102Lys missense_variant 0.22
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
gid 4408297 c.-95G>A upstream_gene_variant 0.12