TB-Profiler result

Run: SRR6257042
Summary

Run ID: SRR6257042

Sample name:

Date: 04-04-2023 13:24:01

Number of reads: 850085

Percentage reads mapped: 98.98

Strain: lineage4.3.3

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 0.98
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.98
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 761139 p.His445Asp missense_variant 0.11 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.87 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288920 p.Gly108Arg missense_variant 1.0 pyrazinamide
embB 4247469 p.Tyr319Ser missense_variant 0.97 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
gyrB 7170 p.Ala644Asp missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766487 p.Pro1040Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776307 p.Asp725Val missense_variant 0.13
mmpL5 778144 p.Ile113Phe missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303095 c.165G>A synonymous_variant 1.0
fbiC 1303897 c.967C>T synonymous_variant 1.0
fbiC 1304962 p.Trp678Gly missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834836 p.Met432Thr missense_variant 0.94
rpsA 1834977 p.Gly479Asp missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.15
PPE35 2169910 p.Asn235Tyr missense_variant 0.2
PPE35 2170147 p.Ser156Ala missense_variant 0.11
PPE35 2170157 p.Ala152Ser missense_variant 0.12
PPE35 2170385 c.228G>T synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518864 c.750G>C synonymous_variant 0.14
kasA 2518879 c.765A>G synonymous_variant 0.12
kasA 2518882 c.768C>A synonymous_variant 0.12
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2746340 p.Ala420Val missense_variant 0.88
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
thyX 3067451 c.495G>A synonymous_variant 0.13
thyA 3073868 p.Thr202Ala missense_variant 0.91
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448878 c.375C>T synonymous_variant 0.12
Rv3083 3449144 p.Pro214Gln missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612021 p.Gly366Ser missense_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038968 c.1737G>A synonymous_variant 1.0
embC 4240476 p.Ala205Val missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245555 p.Glu775Lys missense_variant 0.12
embB 4246845 p.Leu111Ser missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.92