TB-Profiler result

Run: SRR4033466

Summary

Run ID: SRR4033466

Sample name:

Date: 04-04-2023 06:06:59

Number of reads: 1347034

Percentage reads mapped: 99.67

Strain: lineage4.3.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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 2154065 c.2046delT frameshift_variant 0.12 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 5520 p.Pro94Leu missense_variant 1.0
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 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776697 p.Pro595Leu missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461084 p.Gly14* stop_gained 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472190 n.345G>T non_coding_transcript_exon_variant 0.18
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1472846 n.1001C>G non_coding_transcript_exon_variant 0.1
rpsA 1833812 p.Leu91Phe missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168262 c.2347_2350delGGGT frameshift_variant 0.12
PPE35 2169866 c.747G>C synonymous_variant 0.2
Rv1979c 2222640 c.523_524delTC frameshift_variant 0.12
Rv1979c 2222899 p.Arg89Gln missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288863 p.Glu127* stop_gained 0.12
kasA 2518412 p.Ser100Gly missense_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074001 c.471C>T synonymous_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448888 p.Arg129Trp missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474898 p.Gly298Ser missense_variant 0.11
clpC1 4038287 c.2418C>T synonymous_variant 1.0
panD 4043967 c.315C>T synonymous_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4268397 c.439delT frameshift_variant 0.11
ubiA 4269529 p.Ala102Gly missense_variant 0.12
ethA 4327546 c.-73T>C upstream_gene_variant 0.11
ethA 4328247 c.-774G>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407953 p.Pro84Ser missense_variant 0.11
gid 4408156 p.Leu16Arg missense_variant 1.0