TB-Profiler result

Run: ERR2984789
Summary

Run ID: ERR2984789

Sample name:

Date: 01-04-2023 00:06:25

Number of reads: 940127

Percentage reads mapped: 96.68

Strain: lineage4.3.4.1

Drug-resistance: Pre-XDR-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
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 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
gyrA 7566 p.Asp89Asn missense_variant 0.83 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.16 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Asn missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326300 p.Thr392Ala missense_variant 0.11 ethionamide
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 5409 p.Ala57Val missense_variant 0.33
gyrB 6956 c.1719delG frameshift_variant 0.13
gyrB 6965 p.Ser576Arg missense_variant 0.13
gyrB 7220 p.Ser661Gly missense_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7450 p.Pro50Leu missense_variant 0.11
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8259 p.Arg320Cys missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 760319 c.513C>T synonymous_variant 0.4
rpoB 761998 p.Leu731Pro missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765448 c.2079G>A synonymous_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778186 p.Arg99Trp missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781802 c.243G>C synonymous_variant 0.11
rpsL 781805 c.246G>T synonymous_variant 0.11
rpsL 781811 c.252C>T synonymous_variant 0.12
rpsL 781814 c.255C>T synonymous_variant 0.13
rpsL 781817 c.258G>T synonymous_variant 0.13
embR 1417123 c.225C>T synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.33
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.4
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.4
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.5
rrl 1474883 n.1226T>C non_coding_transcript_exon_variant 0.5
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.57
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.5
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.4
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.4
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.4
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.5
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.5
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.5
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.5
inhA 1673497 c.-705G>A upstream_gene_variant 0.11
fabG1 1673728 p.Leu97Phe missense_variant 0.13
inhA 1674758 p.Ser186Leu missense_variant 0.12
inhA 1674840 c.639C>T synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155949 p.Ala55Thr missense_variant 0.12
PPE35 2167767 p.Gly949Asp missense_variant 0.12
PPE35 2168430 p.Gly728Val missense_variant 0.2
PPE35 2168760 p.Pro618Leu missense_variant 0.2
PPE35 2168881 p.Ala578Ser missense_variant 0.29
Rv1979c 2222026 p.Ile380Asn missense_variant 0.22
Rv1979c 2222695 p.Arg157Gln missense_variant 0.2
Rv1979c 2222854 p.Ile104Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726753 c.563delG frameshift_variant 0.15
folC 2747439 p.Met54Leu missense_variant 0.1
Rv2752c 3064865 p.Pro443Ser missense_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086995 p.Gly59Ala missense_variant 0.1
ald 3087620 c.804_819dupCATCGACCAGGGCGGC frameshift_variant 0.96
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039335 p.Leu457Pro missense_variant 0.11
clpC1 4039991 c.714G>A synonymous_variant 1.0
clpC1 4040300 c.405C>G synonymous_variant 1.0
clpC1 4040814 c.-110G>A upstream_gene_variant 0.13
clpC1 4040835 c.-131G>A upstream_gene_variant 0.12
clpC1 4040849 c.-145T>A upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267076 c.1761C>T synonymous_variant 0.13
aftB 4267279 p.Arg520Trp missense_variant 0.12
ethA 4326986 p.His163Leu missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0