TB-Profiler result

Run: SRR6824520
Summary

Run ID: SRR6824520

Sample name:

Date: 04-04-2023 16:43:23

Number of reads: 11504968

Percentage reads mapped: 99.11

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 761095 p.Leu430Pro missense_variant 1.0 rifampicin
rpoB 761110 p.Asp435Gly missense_variant 1.0 rifampicin
rpoB 761115 p.Asn437Asp missense_variant 1.0 rifampicin
katG 2155842 p.Trp90* stop_gained 1.0 isoniazid
pncA 2288934 p.Tyr103Cys missense_variant 0.8 pyrazinamide
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 6754 c.-548C>T upstream_gene_variant 1.0
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
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763730 p.Ala121Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
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
rpsA 1833603 p.Asp21Gly missense_variant 0.13
rpsA 1833813 p.Leu91Arg missense_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288968 p.Ala92Pro missense_variant 0.18
ahpC 2726121 c.-72_-71insT upstream_gene_variant 1.0
Rv2752c 3064516 c.1676A>G splice_region_variant&stop_retained_variant 1.0
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
alr 3841009 p.Leu138Phe missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326676 p.Ser266Arg missense_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407797 p.Ser136Ala missense_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0
whiB6 4337692 c.-1271_*478del transcript_ablation 1.0