TB-Profiler result

Run: SRR1173106
Summary

Run ID: SRR1173106

Sample name:

Date: 03-04-2023 03:16:41

Number of reads: 371060

Percentage reads mapped: 94.84

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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
ethA 4327484 c.-11A>G upstream_gene_variant 1.0 ethionamide
pncA 2288565 c.377_*115del frameshift_variant&stop_lost&splice_region_variant 1.0 pyrazinamide
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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 759888 p.Gly28* stop_gained 0.2
rpoC 763835 p.Ala156Met missense_variant 0.17
rpoC 763853 p.Val162Ile missense_variant 0.17
rpoC 763858 c.489A>G synonymous_variant 0.17
rpoC 763872 p.Gly168Ala missense_variant 0.2
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766488 p.Pro1040Arg missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304517 c.1587C>T synonymous_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.14
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.12
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.12
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169317 c.1296C>T synonymous_variant 0.22
PPE35 2169320 p.Leu431Phe missense_variant 0.25
Rv1979c 2223051 p.Glu38Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
Rv2752c 3065787 c.405G>T synonymous_variant 0.5
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449157 p.Phe218Leu missense_variant 0.17
Rv3083 3449954 p.His484Arg missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038987 p.Asp573Gly missense_variant 0.33
embC 4241137 c.1275G>C synonymous_variant 0.25
embC 4241302 c.1440C>T synonymous_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247985 p.Thr491Ile missense_variant 0.22
aftB 4267656 p.Gly394Val missense_variant 0.29
ethA 4326777 p.Met233Leu missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4407912 c.160_290del frameshift_variant 1.0