TB-Profiler result

Run: SRR15399219
Summary

Run ID: SRR15399219

Sample name:

Date: 03-04-2023 14:10:49

Number of reads: 5772943

Percentage reads mapped: 99.73

Strain: lineage4.3.4.2

Drug-resistance: HR-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
lineage4.3.4 Euro-American (LAM) LAM RD174 0.97
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.97
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
fabG1 1673423 c.-17G>T upstream_gene_variant 0.98 isoniazid, 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
gyrB 5076 c.-164_-163insT upstream_gene_variant 0.98
gyrB 6140 p.Val301Leu missense_variant 0.98
gyrA 6580 c.-722C>G upstream_gene_variant 0.95
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 0.96
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
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.5
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.4
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.33
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.33
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.33
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.25
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.25
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.25
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.29
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.33
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.97
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 0.97
fbiA 3640390 c.-153A>G upstream_gene_variant 0.98
alr 3840719 c.702A>G synonymous_variant 0.98
clpC1 4038287 c.2418C>T synonymous_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.99