TB-Profiler result

Run: SRR3732713
Summary

Run ID: SRR3732713

Sample name:

Date: 04-04-2023 05:38:47

Number of reads: 2072550

Percentage reads mapped: 99.69

Strain: lineage4.8

Drug-resistance: Sensitive

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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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
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 5620 c.381G>T synonymous_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoC 765836 p.Leu823Met missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776032 p.Gly817Trp missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303587 c.657G>A synonymous_variant 0.29
fbiC 1305010 p.Val694Leu missense_variant 0.13
Rv1258c 1406754 p.Ala196Asp missense_variant 0.12
Rv1258c 1407399 c.-59C>A upstream_gene_variant 0.13
embR 1416936 p.Leu138Met missense_variant 0.13
embR 1417219 c.129C>A synonymous_variant 0.18
rrs 1471657 n.-188_-187delTC upstream_gene_variant 1.0
rrs 1471657 n.-187C>T upstream_gene_variant 1.0
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.15
rrs 1473015 n.1170G>T non_coding_transcript_exon_variant 0.2
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476129 n.2472G>A non_coding_transcript_exon_variant 0.2
inhA 1673529 c.-673G>T upstream_gene_variant 0.15
fabG1 1673557 p.His40Asn missense_variant 0.17
inhA 1673591 c.-611C>T upstream_gene_variant 0.15
rpsA 1833421 c.-121C>T upstream_gene_variant 0.13
rpsA 1833787 c.246C>A synonymous_variant 0.14
rpsA 1833801 p.Glu87Val missense_variant 0.17
rpsA 1833901 p.Lys120Asn missense_variant 0.12
rpsA 1833959 p.Leu140Ile missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102374 c.669G>T synonymous_variant 0.2
katG 2154994 p.Arg373His missense_variant 0.12
katG 2156170 c.-59C>A upstream_gene_variant 0.12
PPE35 2167968 p.Pro882Gln missense_variant 0.13
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2168448 p.Gln722Arg missense_variant 0.18
PPE35 2169257 p.Gln452His missense_variant 0.18
PPE35 2169971 c.642T>C synonymous_variant 1.0
Rv1979c 2222469 p.Phe232Leu missense_variant 0.12
Rv1979c 2222856 c.309C>A synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289334 c.-93T>C upstream_gene_variant 0.12
pncA 2289841 c.-600G>T upstream_gene_variant 0.15
kasA 2518264 c.150C>T synonymous_variant 0.18
ahpC 2726425 p.Arg78His missense_variant 0.14
ahpC 2726437 p.Ile82Thr missense_variant 0.12
folC 2746293 p.Leu436Met missense_variant 0.14
Rv2752c 3065351 p.Val281Leu missense_variant 0.11
Rv2752c 3065672 p.Asp174Tyr missense_variant 0.15
Rv2752c 3066088 p.Glu35Gly missense_variant 0.14
ald 3086977 p.Ala53Val missense_variant 0.17
fbiA 3640594 p.Gly18Trp missense_variant 0.14
rpoA 3877489 p.Asp340Val missense_variant 0.12
rpoA 3878237 p.Glu91* stop_gained 0.15
rpoA 3878529 c.-22G>T upstream_gene_variant 0.29
ddn 3986911 p.Arg23Gln missense_variant 0.13
clpC1 4038428 c.2277G>C synonymous_variant 0.13
clpC1 4039729 p.Asp326Asn missense_variant 1.0
clpC1 4040022 p.Gly228Val missense_variant 0.15
clpC1 4040386 p.His107Tyr missense_variant 0.12
clpC1 4040614 p.Glu31* stop_gained 0.14
embC 4241511 p.Met550Lys missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244821 p.Gly530Val missense_variant 0.15
embA 4245244 p.Ala671Val missense_variant 0.13
embB 4246164 c.-350T>C upstream_gene_variant 0.12
embB 4248764 p.Asp751Tyr missense_variant 0.13
embB 4248872 p.Gly787Cys missense_variant 0.18
ethR 4327574 p.Ala9Asp missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0