TB-Profiler result

Run: SRR22424940

Summary

Run ID: SRR22424940

Sample name:

Date: 04-04-2023 04:17:36

Number of reads: 663798

Percentage reads mapped: 99.58

Strain: lineage4.1.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 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
ahpC 2726145 c.-48G>A upstream_gene_variant 0.31 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
gyrA 7234 c.-68C>T upstream_gene_variant 0.12
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 765150 p.Gly594Glu missense_variant 1.0
rpoC 766909 c.3540G>T synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407302 c.39G>T synonymous_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472237 n.392A>G non_coding_transcript_exon_variant 0.13
rrl 1475808 n.2151A>T non_coding_transcript_exon_variant 0.18
inhA 1674769 c.570dupC frameshift_variant 0.11
rpsA 1833534 c.-8C>A upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155301 p.Thr271Pro missense_variant 1.0
PPE35 2167877 p.Ser912Arg missense_variant 0.12
PPE35 2167901 c.2712T>A synonymous_variant 0.12
PPE35 2168318 c.2295T>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289417 c.-176G>A upstream_gene_variant 0.12
ahpC 2726776 p.Ala195Gly missense_variant 0.28
thyX 3067542 p.Ala135Val missense_variant 0.12
thyA 3073862 p.Gly204Cys missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474052 p.Phe16Leu missense_variant 0.11
whiB7 3568637 c.43T>C synonymous_variant 0.12
fbiA 3641447 p.Thr302Met missense_variant 1.0
fbiA 3641533 p.Ala331Thr missense_variant 1.0
alr 3840864 p.Asp186Gly missense_variant 1.0
rpoA 3877553 p.Glu319Lys missense_variant 0.95
embC 4240390 p.Asn176Lys missense_variant 1.0
embC 4240897 c.1035C>G synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243201 c.-31_-30delCC upstream_gene_variant 0.72
embA 4244965 p.Ala578Val missense_variant 0.14
embB 4249408 c.2895G>A synonymous_variant 1.0
ethA 4327161 p.Ile105Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407551 p.Met218Val missense_variant 1.0