TB-Profiler result

Run: ERR4828952
Summary

Run ID: ERR4828952

Sample name:

Date: 01-04-2023 19:11:29

Number of reads: 1019250

Percentage reads mapped: 99.61

Strain: lineage4.1.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4249583 p.Asp1024Asn 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761199 p.Glu465Gln missense_variant 1.0
rpoB 761698 p.Asp631Gly missense_variant 1.0
rpoB 763056 p.Thr1084Pro missense_variant 0.13
rpoB 763144 p.Glu1113Gly missense_variant 0.1
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779011 p.Asp8Asn missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475451 n.1794T>C non_coding_transcript_exon_variant 0.17
inhA 1674686 p.Thr162Met missense_variant 0.12
rpsA 1833759 p.Asp73Val missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102367 p.Ala226Pro missense_variant 0.1
katG 2154796 p.Gln439Arg missense_variant 0.11
PPE35 2167955 c.2658A>C synonymous_variant 0.22
PPE35 2167965 p.Ala883Gly missense_variant 0.22
PPE35 2167967 c.2646A>C synonymous_variant 0.2
PPE35 2168049 p.Gly855Asp missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067899 p.Asp16Val missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641447 p.Thr302Met missense_variant 1.0
alr 3840864 p.Asp186Gly missense_variant 1.0
rpoA 3877553 p.Glu319Lys missense_variant 1.0
embC 4240390 p.Asn176Lys missense_variant 1.0
embC 4240897 c.1035C>G synonymous_variant 1.0
embC 4241886 p.Leu675Pro missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4267005 p.Val611Ala missense_variant 0.11
aftB 4267227 p.Val537Ala missense_variant 0.11
aftB 4267747 p.Ser364Ala missense_variant 1.0
aftB 4267754 c.1082delA frameshift_variant 0.14
aftB 4268055 p.Asn261Ser missense_variant 0.1
aftB 4268606 p.Met77Ile missense_variant 0.29
ethA 4326129 p.Gln449* stop_gained 1.0
ethA 4327161 p.Ile105Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407551 p.Met218Val missense_variant 1.0