TB-Profiler result

Run: SRR20139553
Summary

Run ID: SRR20139553

Sample name:

Date: 03-04-2023 21:49:24

Number of reads: 1814889

Percentage reads mapped: 99.72

Strain: lineage4.8

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
lineage4.8 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 761128 p.Ser441Leu missense_variant 1.0 rifampicin
katG 2154250 c.1861dupG frameshift_variant 1.0 isoniazid
gid 4408100 c.102delG 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 6922 c.-380G>T upstream_gene_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576710 p.Arg455Gly missense_variant 0.18
mshA 576741 p.Ala465Gly missense_variant 0.21
mshA 576744 p.Val466Gly missense_variant 0.19
mshA 576751 p.Lys468Asn missense_variant 0.16
rpoC 765065 p.Leu566Val 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 0.32
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102497 c.546T>G synonymous_variant 0.18
ndh 2103225 c.-183A>C upstream_gene_variant 0.23
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714566 p.Leu256Pro missense_variant 0.17
ahpC 2726100 c.-93_-92insGT upstream_gene_variant 0.96
ahpC 2726338 p.Val49Gly missense_variant 0.23
ahpC 2726341 p.Val50Gly missense_variant 0.28
ahpC 2726345 c.153C>T synonymous_variant 0.17
ahpC 2726350 p.Trp53Leu missense_variant 0.32
ribD 2987323 p.Val162Gly missense_variant 0.18
Rv2752c 3065054 p.Glu380Lys missense_variant 1.0
thyA 3074608 c.-137A>G upstream_gene_variant 0.24
thyA 3074641 c.-170C>T upstream_gene_variant 0.25
thyA 3074645 c.-174T>G upstream_gene_variant 0.27
thyA 3074648 c.-177T>G upstream_gene_variant 0.4
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269864 c.-31C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0