TB-Profiler result

Run: SRR2101560
Summary

Run ID: SRR2101560

Sample name:

Date: 03-04-2023 23:47:23

Number of reads: 581737

Percentage reads mapped: 99.68

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 0.12 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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471775 n.-71G>A upstream_gene_variant 0.13
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1474268 n.611C>A non_coding_transcript_exon_variant 0.17
rrl 1474538 n.881A>G non_coding_transcript_exon_variant 0.12
rrl 1474608 n.951T>C non_coding_transcript_exon_variant 0.12
rrl 1475799 n.2142G>T non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918638 c.699A>C synonymous_variant 0.12
ndh 2101913 c.1129delT frameshift_variant 0.14
PPE35 2168061 p.Ile851Asn missense_variant 0.15
PPE35 2168284 p.Asp777Asn missense_variant 0.12
PPE35 2168738 c.1875T>C synonymous_variant 0.15
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
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086641 c.-179T>C upstream_gene_variant 0.2
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 0.13
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244290 p.Gly353Val missense_variant 0.13
embB 4249492 c.2979C>A synonymous_variant 0.13
aftB 4267087 p.Leu584Met missense_variant 0.15
aftB 4268898 c.-62G>T upstream_gene_variant 0.11
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