TB-Profiler result

Run: SRR6832142
Summary

Run ID: SRR6832142

Sample name:

Date: 04-04-2023 17:15:06

Number of reads: 676575

Percentage reads mapped: 99.41

Strain: lineage4.2.1.1

Drug-resistance: HR-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
lineage4.2.1 Euro-American (TUR) H3;H4 None 1.0
lineage4.2.1.1 Euro-American (TUR) H3;H4 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
katG 2155584 p.Met176Ile missense_variant 0.2 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 6091 c.852G>T synonymous_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7934 c.633C>T synonymous_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9816 c.2515T>G stop_lost&splice_region_variant 0.15
fgd1 491329 p.Lys183* stop_gained 0.18
rpoB 760761 p.Gly319Ser missense_variant 0.22
rpoB 762338 c.2532T>A synonymous_variant 0.15
rpoC 762854 c.-516G>T upstream_gene_variant 0.14
rpoB 762973 p.Gln1056Arg missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776208 p.Leu758Arg missense_variant 0.12
mmpL5 777204 p.Pro426Leu missense_variant 0.2
mmpL5 777451 p.Val344Leu missense_variant 0.86
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407144 p.Val66Asp missense_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472207 n.362A>C non_coding_transcript_exon_variant 0.22
rrs 1472482 n.637G>A non_coding_transcript_exon_variant 0.15
rrs 1472630 n.785A>C non_coding_transcript_exon_variant 0.2
fabG1 1673407 c.-33G>A upstream_gene_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746417 c.1182G>A synonymous_variant 0.13
ribD 2986830 c.-9A>G upstream_gene_variant 0.17
thyX 3067438 p.Ala170Pro missense_variant 0.15
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.8
ald 3087793 p.Ala325Val missense_variant 0.22
fbiD 3339200 p.Pro28Leu missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612767 p.Ala117Val missense_variant 0.18
Rv3236c 3613192 c.-76G>A upstream_gene_variant 0.25
embC 4240030 c.169_171delGCG conservative_inframe_deletion 0.2
embC 4241529 p.Arg556Leu missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245299 c.2067A>C synonymous_variant 0.25
embB 4247531 p.Met340Val missense_variant 0.18
embB 4249149 p.Ala879Gly missense_variant 0.15
aftB 4268875 c.-39G>T upstream_gene_variant 0.25
ethR 4327192 c.-357G>A upstream_gene_variant 0.14
ethR 4327438 c.-111A>G upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 1.0