TB-Profiler result

Run: SRR1146278
Summary

Run ID: SRR1146278

Sample name:

Date: 02-04-2023 21:19:59

Number of reads: 1064254

Percentage reads mapped: 99.33

Strain: lineage4;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 0.16
lineage4 Euro-American LAM;T;S;X;H None 0.89
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.21
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.13
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 761004 p.Thr400Ala missense_variant 0.77 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764822 p.Asp485Asn missense_variant 0.18 rifampicin
mmpR5 779181 c.198dupG frameshift_variant 0.81 clofazimine, bedaquiline
rpsL 781687 p.Lys43Arg missense_variant 0.36 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.63 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155109 p.Ile335Val missense_variant 0.29 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288887 p.Trp119Gly missense_variant 0.67 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.79 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.24 ethambutol
ethA 4326505 c.966_968dupGAC disruptive_inframe_insertion 0.47 ethionamide
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 490751 c.-32T>G upstream_gene_variant 0.6
fgd1 491742 c.960T>C synonymous_variant 0.29
mshA 575837 c.490C>T synonymous_variant 0.75
rpoB 761889 p.Val695Leu missense_variant 0.72
rpoC 763031 c.-339T>C upstream_gene_variant 0.38
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.15
mmpL5 777875 c.605delG frameshift_variant 0.77
mmpS5 779615 c.-710C>G upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801009 c.201A>G synonymous_variant 0.75
fbiC 1303152 c.222C>G synonymous_variant 0.25
Rv1258c 1406760 c.580_581insC frameshift_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 0.96
rpsA 1834177 c.636A>C synonymous_variant 0.38
rpsA 1834776 p.Ala412Val missense_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101831 c.1212G>A synonymous_variant 0.73
katG 2154724 p.Arg463Leu missense_variant 0.19
katG 2156173 c.-62C>A upstream_gene_variant 0.78
PPE35 2167926 p.Leu896Ser missense_variant 0.29
Rv1979c 2223214 c.-50A>C upstream_gene_variant 0.77
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726141 c.-52C>A upstream_gene_variant 0.48
Rv2752c 3065517 c.675C>T synonymous_variant 0.84
thyA 3074495 c.-24C>T upstream_gene_variant 0.86
ald 3086788 c.-32T>C upstream_gene_variant 0.28
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.21
fprA 3474299 p.Asp98Gly missense_variant 0.73
Rv3236c 3612219 p.Val300Ile missense_variant 0.83
Rv3236c 3612813 p.Thr102Ala missense_variant 0.32
fbiB 3640879 c.-656C>T upstream_gene_variant 0.17
rpoA 3878635 c.-128C>T upstream_gene_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 0.15
ethA 4326474 p.Pro334Ala missense_variant 0.29
ethA 4328317 c.-844C>T upstream_gene_variant 0.78
ethA 4328472 c.-999G>T upstream_gene_variant 0.5
whiB6 4338326 p.Ala66Thr missense_variant 0.21
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.28
gid 4407927 p.Glu92Asp missense_variant 0.22
gid 4407967 p.Leu79Trp missense_variant 0.81