TB-Profiler result

Run: ERR5530526
Summary

Run ID: ERR5530526

Sample name:

Date: 01-04-2023 22:33:52

Number of reads: 956590

Percentage reads mapped: 42.24

Strain: lineage4.3.3

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.67 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 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
gyrB 6207 p.Ala323Val missense_variant 0.12
gyrB 7152 p.Leu638Arg missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490756 c.-27T>G upstream_gene_variant 0.18
fgd1 491070 c.288G>T synonymous_variant 0.14
mshA 576108 p.Ala254Gly missense_variant 0.44
mshA 576113 p.Arg256Gly missense_variant 0.27
mshA 576456 p.Val370Gly missense_variant 0.18
mshA 576479 p.Pro378Ala missense_variant 0.18
ccsA 620758 p.Arg290Cys missense_variant 0.11
rpoC 764661 c.1294delG frameshift_variant 0.17
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776697 p.Pro595Leu missense_variant 0.22
mmpL5 777883 p.Gly200Arg missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781921 c.364delG frameshift_variant 0.15
embR 1417174 c.174C>T synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.67
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.67
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.67
rrs 1472674 n.829T>A non_coding_transcript_exon_variant 0.67
rrs 1472675 n.830T>A non_coding_transcript_exon_variant 0.67
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.67
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.67
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.5
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.5
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.5
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.5
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.4
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.5
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.5
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.5
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.67
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.5
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.38
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.5
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.86
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.88
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.8
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.67
rpsA 1833724 c.183C>A synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918602 c.663C>T synonymous_variant 0.11
ndh 2101671 p.Ser458Gly missense_variant 0.11
PPE35 2170065 p.Ala183Gly missense_variant 0.38
Rv1979c 2222559 c.606G>A synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
eis 2715314 p.Ser7Gly missense_variant 0.11
pepQ 2859371 p.Lys350* stop_gained 0.12
pepQ 2860159 p.Ala87Gly missense_variant 0.21
ribD 2987506 p.Leu223Arg missense_variant 0.27
Rv2752c 3065874 p.Lys106Asn missense_variant 0.13
Rv2752c 3066313 c.-122T>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086646 c.-174G>T upstream_gene_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087816 p.Cys333Gly missense_variant 0.17
fbiD 3339734 p.Ala206Gly missense_variant 0.5
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039013 c.1691delA frameshift_variant 0.22
embC 4240409 p.Pro183Ala missense_variant 0.2
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243185 c.-48G>A upstream_gene_variant 0.13
embA 4245182 c.1950T>C synonymous_variant 0.12
embB 4246527 p.Ala5Gly missense_variant 0.4
embB 4248412 p.Phe633Leu missense_variant 0.2
embB 4249761 p.Ala1083Val missense_variant 0.12
ethA 4326244 p.Asp410Glu missense_variant 0.25
ethR 4327639 c.93delC frameshift_variant 0.12
ethR 4327774 p.Leu76Met missense_variant 0.1
whiB6 4338398 p.Thr42Ala missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0