TB-Profiler result

Run: SRR1169187
Summary

Run ID: SRR1169187

Sample name:

Date: 03-04-2023 02:48:50

Number of reads: 779320

Percentage reads mapped: 98.74

Strain: lineage4.3.4.2.1

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
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
thyX 3067961 c.-16C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
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 5227 c.-13G>T upstream_gene_variant 0.12
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620001 c.111C>T synonymous_variant 1.0
rpoB 760400 c.594G>T synonymous_variant 0.1
rpoC 764670 p.Pro434Leu missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777100 p.Asp461Tyr missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476420 n.2763G>T non_coding_transcript_exon_variant 0.13
fabG1 1673577 p.His46Gln missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101716 p.Glu443* stop_gained 0.17
katG 2156062 p.Ser17Ile missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289706 c.-465C>G upstream_gene_variant 0.15
eis 2714633 p.Lys234Glu missense_variant 0.23
thyA 3073696 p.Ala259Val missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087836 c.1017A>G synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiA 3641404 p.Trp288Arg missense_variant 0.17
alr 3840719 c.702A>G synonymous_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245190 p.Leu653Pro missense_variant 1.0
ethA 4326128 p.Gln449Arg missense_variant 0.12
ethA 4328079 c.-606C>A upstream_gene_variant 0.14
whiB6 4338593 c.-73delT upstream_gene_variant 1.0
whiB6 4338596 c.-75G>C upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0