TB-Profiler result

Run: SRR21675708
Summary

Run ID: SRR21675708

Sample name:

Date: 04-04-2023 02:38:20

Number of reads: 627749

Percentage reads mapped: 99.56

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
gid 4408100 c.102delG frameshift_variant 0.94 streptomycin
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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491253 c.471C>G synonymous_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575423 p.Arg26Cys missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
ccsA 619831 c.-60T>G upstream_gene_variant 0.18
rpoB 760115 c.309C>T synonymous_variant 0.93
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777680 c.801G>T synonymous_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475178 n.1521T>C non_coding_transcript_exon_variant 0.22
inhA 1674194 c.-8G>T upstream_gene_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102902 c.141C>A synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517983 c.-132T>A upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339741 c.624G>T synonymous_variant 0.12
fbiD 3339744 c.627A>C synonymous_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568585 p.Thr32Asn missense_variant 0.11
Rv3236c 3612322 c.795G>A synonymous_variant 0.13
clpC1 4039484 c.1221T>G synonymous_variant 0.3
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0