TB-Profiler result

Run: SRR16157124
Summary

Run ID: SRR16157124

Sample name:

Date: 03-04-2023 16:44:20

Number of reads: 956644

Percentage reads mapped: 99.04

Strain: lineage4.1.1.3

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.99
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 761139 p.His445Asn missense_variant 0.26 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.78 rifampicin
katG 2154095 c.2016delA frameshift_variant 0.12 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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766740 p.Val1124Ala missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777691 p.Asn264Asp missense_variant 0.12
mmpR5 779291 p.Ala101Glu missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407385 c.-45G>T upstream_gene_variant 1.0
atpE 1461050 c.6C>T synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476760 n.3103A>T non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154678 c.1434G>C synonymous_variant 1.0
PPE35 2169919 p.Leu232Phe missense_variant 0.25
PPE35 2170303 p.Met104Leu missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290067 c.-826C>A upstream_gene_variant 0.15
ahpC 2726409 p.Asp73His missense_variant 1.0
pepQ 2860072 p.Gly116Val missense_variant 0.96
Rv2752c 3064858 p.Gly445Ala missense_variant 0.11
Rv2752c 3066369 c.-178C>G upstream_gene_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640813 p.Glu91Gln missense_variant 0.12
fbiB 3642123 p.Glu197Lys missense_variant 0.13
rpoA 3877871 p.Lys213Glu missense_variant 0.11
rpoA 3878167 p.Ala114Val missense_variant 0.15
rpoA 3878630 c.-123G>C upstream_gene_variant 0.23
rpoA 3878635 c.-128C>G upstream_gene_variant 0.14
embC 4242065 p.Ser735Pro missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246319 c.-195G>A upstream_gene_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
embB 4249678 c.3165C>A synonymous_variant 1.0
aftB 4268205 p.Val211Gly missense_variant 0.11
ethA 4327458 p.Asp6Asn missense_variant 0.13
ethA 4327487 c.-14G>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0