TB-Profiler result

Run: SRR20139570
Summary

Run ID: SRR20139570

Sample name:

Date: 03-04-2023 21:50:44

Number of reads: 2641609

Percentage reads mapped: 99.66

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
pncA 2288778 p.Val155Gly missense_variant 1.0 pyrazinamide
ahpC 2726136 c.-57C>T upstream_gene_variant 1.0 isoniazid
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 6922 c.-380G>T upstream_gene_variant 0.17
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 0.18
fgd1 490756 c.-27T>G upstream_gene_variant 0.16
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 0.99
mshA 576744 p.Val466Gly missense_variant 0.14
ccsA 620748 c.858T>G synonymous_variant 0.23
rpoB 759615 c.-192A>C upstream_gene_variant 0.34
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304159 p.Val410Gly missense_variant 0.25
fbiC 1304166 c.1236A>G synonymous_variant 0.17
fbiC 1304186 p.Asp419Gly missense_variant 0.16
Rv1258c 1407055 p.Tyr96Asp missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473953 n.296T>G non_coding_transcript_exon_variant 0.18
rrl 1474039 n.382A>G non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154403 p.Gly570Ala missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.17
ahpC 2726341 p.Val50Gly missense_variant 0.25
ahpC 2726350 p.Trp53Leu missense_variant 0.27
ahpC 2726355 p.Lys55Glu missense_variant 0.16
thyA 3074641 c.-170C>T upstream_gene_variant 0.17
thyA 3074645 c.-174T>G upstream_gene_variant 0.23
thyA 3074648 c.-177T>G upstream_gene_variant 0.23
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249305 p.Asn931Thr missense_variant 0.21
embB 4249323 p.Ala937Glu missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407963 c.240G>T synonymous_variant 1.0
gid 4407991 p.Gly71Glu missense_variant 1.0