TB-Profiler result

Run: SRR4033953

Summary

Run ID: SRR4033953

Sample name:

Date: 04-04-2023 06:27:55

Number of reads: 659782

Percentage reads mapped: 99.57

Strain: lineage4.3.2.1

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 0.99
lineage4.3.2 Euro-American (LAM) LAM3 None 0.97
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 0.99
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
ethA 4327036 c.437delG frameshift_variant 0.13 ethionamide
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 5520 p.Pro94Leu missense_variant 1.0
gyrB 5784 p.Thr182Ile missense_variant 0.15
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8033 p.Tyr244* stop_gained 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761844 c.2039delA frameshift_variant 0.13
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765405 c.2039delG frameshift_variant 0.17
rpoC 766433 p.Glu1022Lys missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776446 c.2034delA frameshift_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303226 p.Arg99Leu missense_variant 0.12
fbiC 1304643 c.1713G>A synonymous_variant 0.17
embR 1416792 p.Arg186Trp missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471666 n.-180A>C upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1473261 n.1416G>A non_coding_transcript_exon_variant 0.14
rrs 1473325 n.1480G>T non_coding_transcript_exon_variant 0.13
fabG1 1673806 p.Ala123Thr missense_variant 0.29
fabG1 1673825 p.Arg129His missense_variant 0.22
rpsA 1833951 p.Gly137Val missense_variant 0.2
rpsA 1833977 p.Gly146Cys missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918199 p.Leu87Gln missense_variant 0.18
katG 2154767 p.Leu449Ile missense_variant 0.15
PPE35 2167960 c.2652dupG frameshift_variant 0.13
Rv1979c 2222655 c.509delA frameshift_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726293 p.Tyr34Cys missense_variant 1.0
ribD 2986887 p.Leu17Phe missense_variant 0.12
Rv2752c 3066132 c.60G>A synonymous_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448543 p.Leu14Ile missense_variant 0.13
Rv3083 3448554 c.54dupG frameshift_variant 0.14
Rv3083 3448983 c.480C>A synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474519 c.516_517dupGT frameshift_variant 0.18
fbiA 3640801 p.His87Tyr missense_variant 0.13
fbiA 3641257 p.Pro239Thr missense_variant 0.25
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4240732 p.Asn290Lys missense_variant 0.18
embC 4242579 p.Ala906Val missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245057 p.Ala609Thr missense_variant 0.17
embB 4248193 c.1680C>A synonymous_variant 0.13
ethR 4327951 p.Ala135Ser missense_variant 0.27
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0