TB-Profiler result

Run: SRR12830381

Summary

Run ID: SRR12830381

Sample name:

Date: 03-04-2023 06:58:45

Number of reads: 461783

Percentage reads mapped: 99.8

Strain: lineage4.3.3

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
lineage4.3 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
pncA 2288704 p.Val180Phe missense_variant 0.12 pyrazinamide
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 5505 p.His89Arg missense_variant 0.11
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 9130 c.1831delG frameshift_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575156 c.-192G>C upstream_gene_variant 0.12
mshA 575965 c.618C>T synonymous_variant 0.15
mshA 576310 c.963C>T synonymous_variant 0.13
rpoB 762313 p.Gly836Ala missense_variant 0.1
rpoB 762502 p.Pro899Leu missense_variant 0.13
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407031 p.Leu104Met missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473269 n.1424C>A non_coding_transcript_exon_variant 0.15
rrs 1473334 n.1489C>A non_coding_transcript_exon_variant 0.22
rrl 1473552 n.-106G>T upstream_gene_variant 0.15
rrl 1474908 n.1251G>A non_coding_transcript_exon_variant 0.67
rrl 1474921 n.1264C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102308 c.735G>A synonymous_variant 1.0
katG 2155776 c.336C>A synonymous_variant 0.12
PPE35 2168109 p.Thr835Asn missense_variant 0.17
PPE35 2170093 p.Leu174Ile missense_variant 0.16
Rv1979c 2222420 p.Asp249Asn missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518815 p.Arg234Leu missense_variant 0.15
kasA 2518919 p.Gly269Ser missense_variant 1.0
ahpC 2726645 c.453C>G synonymous_variant 0.11
pepQ 2860494 c.-76T>C upstream_gene_variant 0.14
Rv2752c 3065069 p.His375Tyr missense_variant 0.14
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086964 p.Asp49Asn missense_variant 0.12
Rv3083 3449854 p.Met451Val missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475213 p.Ala403Thr missense_variant 0.12
fbiA 3641293 p.Pro251Ser missense_variant 0.13
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4241698 c.1836G>A synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243178 c.-54delT upstream_gene_variant 0.12
embA 4244883 p.Arg551* stop_gained 0.15
aftB 4267309 p.Leu510Met missense_variant 0.14
ethR 4327559 p.Ser4Tyr missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0