TB-Profiler result

Run: SRR6982041

Summary

Run ID: SRR6982041

Sample name:

Date: 04-04-2023 18:25:34

Number of reads: 518237

Percentage reads mapped: 99.69

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 2155801 p.Arg104Leu missense_variant 0.17 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
gyrB 6227 p.Lys330Glu missense_variant 0.11
gyrB 6700 p.Asn487Lys missense_variant 0.12
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7508 p.Ser69Arg missense_variant 0.13
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7961 p.Met220Ile missense_variant 0.11
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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304405 p.Asp492Gly missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471775 n.-71G>A upstream_gene_variant 0.15
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1474608 n.951T>C non_coding_transcript_exon_variant 0.17
rrl 1475799 n.2142G>T non_coding_transcript_exon_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918638 c.699A>C synonymous_variant 0.15
ndh 2101913 c.1129delT frameshift_variant 0.18
katG 2155291 p.Lys274Arg missense_variant 0.11
PPE35 2168061 p.Ile851Asn missense_variant 0.18
PPE35 2168738 c.1875T>C synonymous_variant 0.17
Rv1979c 2222549 p.Ser206Pro missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289339 c.-98C>A upstream_gene_variant 0.15
eis 2715370 c.-38C>G upstream_gene_variant 0.12
ahpC 2726338 p.Val49Gly missense_variant 0.31
ahpC 2726396 c.205_206delAG frameshift_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086641 c.-179T>C upstream_gene_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449158 p.Ser219Pro missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612534 p.Ala195Thr missense_variant 0.2
Rv3236c 3612659 p.Ser153* stop_gained 0.13
fbiB 3640617 c.-918G>T upstream_gene_variant 0.1
rpoA 3877982 p.Tyr176His missense_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038293 c.2412G>C synonymous_variant 0.1
embC 4242519 p.Thr886Met missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244076 p.Arg282Trp missense_variant 0.11
embA 4244290 p.Gly353Val missense_variant 0.14
embB 4246533 p.Arg7Ile missense_variant 0.11
embB 4249492 c.2979C>A synonymous_variant 0.14
aftB 4268898 c.-62G>T upstream_gene_variant 0.12
ubiA 4268986 p.Val283Ala missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0