TB-Profiler result

Run: SRR14781854
Summary

Run ID: SRR14781854

Sample name:

Date: 03-04-2023 11:02:06

Number of reads: 1183659

Percentage reads mapped: 99.64

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.99
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
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 9647 c.2346C>G synonymous_variant 0.16
fgd1 490756 c.-27T>G upstream_gene_variant 0.25
mshA 576613 c.1266A>C synonymous_variant 0.22
mshA 576616 c.1269G>C synonymous_variant 0.17
rpoB 761482 p.Ala559Gly missense_variant 0.23
rpoC 764367 p.Gly333Ala missense_variant 0.24
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918410 p.Phe157Leu missense_variant 0.18
katG 2155430 p.Ile228Leu missense_variant 0.98
PPE35 2168149 p.Pro822Ser missense_variant 0.95
PPE35 2170065 p.Ala183Gly missense_variant 0.38
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.27
thyA 3074422 p.Pro17Leu missense_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.67
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3474212 p.Lys69Thr missense_variant 0.21
whiB7 3568422 c.258G>C synonymous_variant 0.4
whiB7 3568428 c.252A>G synonymous_variant 0.75
rpoA 3878597 c.-90G>C upstream_gene_variant 0.67
rpoA 3878641 c.-134C>G upstream_gene_variant 0.4
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embC 4240409 p.Pro183Ala missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.55
embB 4247020 c.507C>G synonymous_variant 0.15
embB 4248328 c.1815G>C synonymous_variant 0.15
whiB6 4338200 p.Asp108His missense_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408102 p.Gly34Glu missense_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0