TB-Profiler result

Run: SRR6982323
Summary

Run ID: SRR6982323

Sample name:

Date: 04-04-2023 18:34:04

Number of reads: 826948

Percentage reads mapped: 99.82

Strain: lineage4.3.4.2.1

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
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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 2154025 c.2086delC frameshift_variant 0.11 isoniazid, 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 6140 p.Val301Leu missense_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
fgd1 490751 c.-32T>G upstream_gene_variant 0.24
ccsA 620748 c.858T>G synonymous_variant 0.21
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776065 p.Gly806Ser missense_variant 0.11
mmpR5 779293 p.Ala102Thr missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473959 n.302T>G non_coding_transcript_exon_variant 0.22
rrl 1475114 n.1457C>T non_coding_transcript_exon_variant 1.0
rrl 1476336 n.2679C>A non_coding_transcript_exon_variant 0.14
fabG1 1673930 p.Ala164Val missense_variant 0.12
inhA 1674548 p.Val116Gly missense_variant 0.11
tlyA 1917743 c.-197G>T upstream_gene_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101838 c.1204delG frameshift_variant 0.11
PPE35 2167859 c.2754T>G synonymous_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
alr 3840719 c.702A>G synonymous_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
panD 4043938 p.Ile115Thr missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244742 p.Phe504Leu missense_variant 0.1
embA 4244963 p.Phe577Leu missense_variant 0.12
ubiA 4269518 p.Ala106Ser missense_variant 0.14
whiB6 4338303 c.219A>G synonymous_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0