TB-Profiler result

Run: SRR4037884
Summary

Run ID: SRR4037884

Sample name:

Date: 04-04-2023 07:44:35

Number of reads: 1039107

Percentage reads mapped: 99.7

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 2154893 c.1218delC frameshift_variant 0.18 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 9036 p.Ala579Thr missense_variant 0.12
gyrA 9300 p.Ala667Pro missense_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491124 c.342C>T synonymous_variant 0.12
rpoC 764671 c.1302G>A synonymous_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778303 p.Gln60Lys missense_variant 0.12
mmpR5 779123 p.Val45Ala missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.12
fbiC 1304965 p.Val679Met missense_variant 0.12
embR 1416677 p.Ala224Glu missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169097 c.1515delG frameshift_variant 0.33
PPE35 2169320 p.Leu431Phe missense_variant 0.4
Rv1979c 2222893 p.Gly91Val missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289496 c.-255G>A upstream_gene_variant 0.17
kasA 2519332 c.1218C>A synonymous_variant 0.13
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339697 p.Asp194Asn missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474360 p.Asp118Glu missense_variant 0.12
Rv3236c 3612523 c.594G>A synonymous_variant 0.17
rpoA 3877851 c.657C>T synonymous_variant 0.13
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.2
clpC1 4039768 p.Ala313Thr missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247171 c.658C>T synonymous_variant 0.22
embB 4249613 p.Gly1034Ser missense_variant 0.11
aftB 4269096 c.-260C>T upstream_gene_variant 0.11
ethA 4327300 p.Asp58Glu missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0