TB-Profiler result

Run: SRR5526360
Summary

Run ID: SRR5526360

Sample name:

Date: 04-04-2023 10:35:05

Number of reads: 660487

Percentage reads mapped: 99.63

Strain: lineage2.2.1.1

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
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674262 p.Ile21Val missense_variant 1.0 isoniazid
pncA 2288960 c.281delT frameshift_variant 0.12 pyrazinamide
pncA 2289040 p.Trp68Arg missense_variant 1.0 pyrazinamide
embB 4248003 p.Gln497Arg 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
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 760634 c.828T>C synonymous_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763947 p.Ala193Glu missense_variant 0.12
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 764962 c.1593G>A synonymous_variant 0.11
rpoC 765384 p.Met672Thr missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777244 p.Thr413Pro missense_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303108 p.Ala60Thr missense_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.33
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102738 c.304delG frameshift_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155907 p.Ala69Ser missense_variant 0.12
katG 2156101 p.Gln4Leu missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.15
PPE35 2170053 p.Thr187Ser missense_variant 0.14
Rv1979c 2222386 c.723C>A synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289517 c.-276C>A upstream_gene_variant 0.14
kasA 2518863 c.754_756delGAG conservative_inframe_deletion 0.12
eis 2714846 p.Val163Ile missense_variant 1.0
folC 2747686 c.-88C>A upstream_gene_variant 0.12
ribD 2987040 c.202C>A synonymous_variant 0.17
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
rpoA 3877698 c.810C>T synonymous_variant 0.12
clpC1 4038368 c.2337T>C synonymous_variant 0.12
clpC1 4039143 p.Gln521Arg missense_variant 0.1
clpC1 4039487 c.1218G>T synonymous_variant 0.13
clpC1 4040397 p.Ile103Thr missense_variant 0.11
clpC1 4040617 p.Thr30Ala missense_variant 0.1
panD 4043992 p.Arg97Pro missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245131 c.1899G>A synonymous_variant 1.0
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4249375 c.2862G>A synonymous_variant 0.12
aftB 4267647 p.Asp397Gly 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
gid 4408453 c.-251G>A upstream_gene_variant 0.11