TB-Profiler result

Run: SRR4035931
Summary

Run ID: SRR4035931

Sample name:

Date: 04-04-2023 07:23:15

Number of reads: 1186979

Percentage reads mapped: 99.69

Strain: lineage4.4.1.1.1

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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 1.0
lineage4.4.1.1.1 Euro-American S;Orphans 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
katG 2153990 c.2121delT frameshift_variant 0.25 isoniazid
katG 2154793 c.1318dupG frameshift_variant 0.11 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 5704 c.465C>A synonymous_variant 0.14
gyrB 7185 p.Ser649Tyr missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8524 c.1225delC frameshift_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9617 c.2316C>T synonymous_variant 0.12
mshA 576073 c.726C>T synonymous_variant 0.15
mmpL5 775597 p.Ala962Ser missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.17
fbiC 1304074 p.Ala382Thr missense_variant 0.13
embR 1416929 p.Ala140Val missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472204 n.359G>T non_coding_transcript_exon_variant 0.25
inhA 1674534 c.333G>A synonymous_variant 0.12
inhA 1674952 p.Pro251Ala missense_variant 0.12
rpsA 1834716 c.1179dupC frameshift_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2153970 p.Asp714Glu missense_variant 0.33
PPE35 2169320 p.Leu431Phe missense_variant 0.25
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714224 p.Ala370Val missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiB 3640683 c.-852C>T upstream_gene_variant 0.15
panD 4044179 p.Ala35Thr missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242748 c.-485A>C upstream_gene_variant 0.14
embB 4246928 p.Gln139Lys missense_variant 0.12
embB 4247161 c.648G>A synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0