TB-Profiler result

Run: ERR2515723

Summary

Run ID: ERR2515723

Sample name:

Date: 31-03-2023 21:05:03

Number of reads: 599064

Percentage reads mapped: 99.69

Strain: lineage2.2.1

Drug-resistance: RR-TB


Download CSV Download TXT Download PDF Download JSON
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 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
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 9549 p.Val750Leu missense_variant 0.11
gyrA 9768 p.Gly823Arg missense_variant 0.13
fgd1 490992 c.210G>T synonymous_variant 0.12
fgd1 491200 c.418C>A synonymous_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576564 p.Leu406Pro missense_variant 0.12
mshA 576587 p.Gly414* stop_gained 0.11
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761297 p.Tyr497* stop_gained 0.12
rpoB 761793 p.Thr663Pro missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765549 p.Ser727Ile missense_variant 0.1
rpoC 766843 c.3474T>A synonymous_variant 0.14
rpoC 766927 c.3558C>T synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpR5 779386 p.Ser133Gly missense_variant 0.29
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406252 p.Gly363Val missense_variant 0.14
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472884 n.1040delT non_coding_transcript_exon_variant 0.11
rrl 1474002 n.345G>A non_coding_transcript_exon_variant 0.12
rrl 1476739 n.3082T>C non_coding_transcript_exon_variant 0.14
inhA 1674099 c.-103G>T upstream_gene_variant 0.14
inhA 1674210 c.9A>C synonymous_variant 1.0
inhA 1674476 p.Val92Ala missense_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103239 c.-197T>C upstream_gene_variant 0.1
katG 2154538 p.Gln525Arg missense_variant 0.1
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170053 p.Thr187Ser missense_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714657 p.Tyr226His missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339244 p.Leu43Phe missense_variant 0.12
Rv3083 3448402 c.-102C>G upstream_gene_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612192 p.Gly309Trp missense_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embC 4241947 c.2088delT frameshift_variant 0.11
embA 4242598 c.-635T>A upstream_gene_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243634 c.404delG frameshift_variant 0.13
embA 4244777 p.Met515Ile missense_variant 0.12
embA 4245443 c.2211C>T synonymous_variant 0.12
embB 4246657 c.144C>A synonymous_variant 0.17
embB 4249333 c.2820C>T synonymous_variant 0.14
embB 4249642 p.Leu1043Phe missense_variant 0.14
aftB 4267507 p.Asn444Asp missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268892 c.-56T>C upstream_gene_variant 0.14
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 4408090 p.Pro38His missense_variant 0.11