TB-Profiler result

Run: SRR6797285
Summary

Run ID: SRR6797285

Sample name:

Date: 04-04-2023 16:04:59

Number of reads: 1018563

Percentage reads mapped: 99.04

Strain: lineage4.1.1.3

Drug-resistance: Other

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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 0.98
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
tlyA 1918634 p.Gly232Asp missense_variant 0.25 capreomycin
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 5198 c.-42C>A upstream_gene_variant 0.12
gyrA 6628 c.-674C>A upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576090 p.Arg248His missense_variant 0.25
rpoB 759732 c.-75C>A upstream_gene_variant 0.2
rpoC 763774 c.406delA frameshift_variant 0.14
rpoC 765150 p.Gly594Glu missense_variant 0.88
rpoC 765258 p.Arg630Leu missense_variant 0.33
rpoC 767172 p.Arg1268His missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776219 c.2262C>A synonymous_variant 0.17
mmpL5 778089 p.Gly131Val missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302743 c.-188C>T upstream_gene_variant 0.14
Rv1258c 1406235 p.Pro369Gln missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472098 n.253G>T non_coding_transcript_exon_variant 0.13
inhA 1674628 p.Ser143Pro missense_variant 0.2
rpsA 1834030 c.490delT frameshift_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2222252 p.Val305Phe missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860238 p.Arg61Ser missense_variant 0.25
ribD 2986966 p.Ala43Val missense_variant 0.12
Rv2752c 3065037 c.1155C>T synonymous_variant 0.14
thyX 3067528 p.Arg140Ser missense_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087042 p.Lys75Glu missense_variant 0.13
ald 3087903 p.Pro362Ser missense_variant 0.25
Rv3083 3449037 p.Lys178Asn missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474089 p.Thr28Lys missense_variant 0.2
fbiB 3641490 c.-45G>C upstream_gene_variant 0.17
fbiB 3641738 c.204G>A synonymous_variant 0.13
alr 3841087 p.Trp112Arg missense_variant 0.17
ddn 3987062 c.219C>A synonymous_variant 0.18
ddn 3987221 p.Leu126Phe missense_variant 0.11
clpC1 4038874 p.Thr611Pro missense_variant 0.18
clpC1 4039354 p.Arg451Cys missense_variant 0.18
clpC1 4040030 c.675C>T synonymous_variant 0.17
embC 4242198 p.Ala779Asp missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4243145 c.3283T>C stop_lost&splice_region_variant 0.2
embA 4243855 p.Leu208His missense_variant 0.2
embA 4244236 p.Cys335Phe missense_variant 0.15
embA 4245564 p.Gly778Cys missense_variant 0.2
embB 4247691 p.Thr393Asn missense_variant 0.17
embB 4248639 p.Ile709Thr missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4268149 p.Gly230Cys missense_variant 0.18
ethA 4326172 p.Phe434Leu missense_variant 0.18
ethR 4327736 p.Phe63Cys missense_variant 0.25
ethA 4328287 c.-814G>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407562 p.Gly214Val missense_variant 0.18