TB-Profiler result

Run: SRR20139562
Summary

Run ID: SRR20139562

Sample name:

Date: 03-04-2023 21:50:12

Number of reads: 2176327

Percentage reads mapped: 99.72

Strain: lineage4.8

Drug-resistance: RR-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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 761086 p.Thr427Ile missense_variant 1.0 rifampicin
rpoB 761277 p.Ile491Phe missense_variant 1.0 rifampicin
pncA 2289234 p.Ala3Glu missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 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 6932 p.Gln565Lys missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 490756 c.-27T>G upstream_gene_variant 0.18
fgd1 490759 c.-24A>T upstream_gene_variant 0.15
fgd1 490771 c.-12T>G upstream_gene_variant 0.16
mshA 576710 p.Arg455Gly missense_variant 0.2
mshA 576732 p.Asp462Ala missense_variant 1.0
mshA 576739 c.1392A>G synonymous_variant 0.2
mshA 576741 p.Ala465Gly missense_variant 0.25
mshA 576744 p.Val466Gly missense_variant 0.16
rpoB 759615 c.-192A>C upstream_gene_variant 0.25
rpoC 763348 c.-22C>T upstream_gene_variant 1.0
rpoC 765689 p.Leu774Val missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779302 p.Arg105Gly missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.16
fbiC 1303055 p.Asp42Gly missense_variant 0.27
fbiC 1304159 p.Val410Gly missense_variant 0.23
fbiC 1304166 c.1236A>G synonymous_variant 0.19
Rv1258c 1407055 p.Tyr96Asp missense_variant 0.21
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102497 c.546T>G synonymous_variant 0.21
ndh 2103225 c.-183A>C upstream_gene_variant 0.16
katG 2155843 p.Trp90Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714524 p.His270Pro missense_variant 0.15
eis 2714549 p.Met262Leu missense_variant 0.14
eis 2714561 p.Gly258Cys missense_variant 0.21
ahpC 2726338 p.Val49Gly missense_variant 0.19
ahpC 2726341 p.Val50Gly missense_variant 0.27
ahpC 2726350 p.Trp53Leu missense_variant 0.31
pepQ 2860451 c.-33G>A upstream_gene_variant 1.0
ribD 2987323 p.Val162Gly missense_variant 0.22
Rv2752c 3067180 c.-989C>A upstream_gene_variant 1.0
thyA 3074595 c.-124C>T upstream_gene_variant 0.16
thyA 3074601 c.-130T>G upstream_gene_variant 0.16
thyA 3074641 c.-170C>T upstream_gene_variant 0.14
thyA 3074645 c.-174T>G upstream_gene_variant 0.2
thyA 3074648 c.-177T>G upstream_gene_variant 0.31
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249305 p.Asn931Thr missense_variant 0.21
embB 4249323 p.Ala937Glu missense_variant 0.21
ethA 4326788 p.Leu229Arg missense_variant 0.87
whiB6 4338593 c.-73delT upstream_gene_variant 1.0
whiB6 4338596 c.-75G>C upstream_gene_variant 1.0
gid 4407991 p.Gly71Glu missense_variant 0.93
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0