TB-Profiler result

Run: SRR3732579
Summary

Run ID: SRR3732579

Sample name:

Date: 04-04-2023 05:36:06

Number of reads: 2374648

Percentage reads mapped: 99.47

Strain: lineage4.3.4.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
gid 4408022 c.180delA frameshift_variant 1.0 streptomycin
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
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765590 p.Arg741Ser missense_variant 1.0
rpoC 765862 p.Phe831Leu missense_variant 0.65
rpoC 766196 p.Asp943Asn missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472416 n.571C>A non_coding_transcript_exon_variant 0.15
rrs 1472717 n.872C>A non_coding_transcript_exon_variant 0.13
rrs 1473022 n.1177G>T non_coding_transcript_exon_variant 0.2
rrl 1473785 n.128C>A non_coding_transcript_exon_variant 0.22
rrl 1476009 n.2352G>T non_coding_transcript_exon_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223123 c.42G>A synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714768 p.Gly189Trp missense_variant 0.12
Rv2752c 3064849 p.Phe448Ser missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.98
Rv3083 3449183 p.Ser227Tyr missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612162 p.Ala319Thr missense_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243033 p.Trp1057Cys missense_variant 0.14
embA 4244858 c.1626G>T synonymous_variant 0.13
whiB6 4338218 p.Asn102Asp missense_variant 1.0
whiB6 4338290 p.Gly78Trp missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0