TB-Profiler result

Run: SRR6832116
Summary

Run ID: SRR6832116

Sample name:

Date: 04-04-2023 17:14:13

Number of reads: 637424

Percentage reads mapped: 99.64

Strain: lineage4.3.3

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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
katG 2155959 c.152delA frameshift_variant 0.25 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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 5922 p.Glu228Gly missense_variant 0.25
gyrB 7058 p.Ile607Val missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491036 p.Val85Gly missense_variant 0.29
rpoB 762958 p.Leu1051Pro missense_variant 0.15
rpoC 764602 c.1233C>T synonymous_variant 0.22
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 1303095 c.165G>A synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474954 n.1297A>T non_coding_transcript_exon_variant 0.14
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102117 p.Leu309Arg missense_variant 0.29
ndh 2102563 c.480G>T synonymous_variant 0.16
katG 2154515 p.Pro533Thr missense_variant 0.33
katG 2155732 p.Gln127Ser missense_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 1.0
PPE35 2167737 p.Leu959Pro missense_variant 0.33
PPE35 2168979 p.Pro545Leu missense_variant 0.25
Rv1979c 2223119 p.Phe16Leu missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2746340 p.Ala420Val missense_variant 1.0
folC 2747461 c.138C>T synonymous_variant 0.12
ribD 2986794 c.-45G>A upstream_gene_variant 0.12
ribD 2986938 p.Tyr34Asn missense_variant 0.2
Rv2752c 3065119 p.Ile358Thr missense_variant 0.15
thyX 3067351 p.Arg199Trp missense_variant 0.29
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086815 c.-5T>G upstream_gene_variant 0.27
Rv3083 3449931 c.1428C>T synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841447 c.-27A>G upstream_gene_variant 0.15
rpoA 3877653 c.855C>T synonymous_variant 0.14
ddn 3987204 c.363delA frameshift_variant 0.29
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038968 c.1737G>A synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243013 p.Asp1051Tyr missense_variant 0.33
embA 4243824 p.Thr198Ala missense_variant 0.29
embA 4246173 p.Ile981Phe missense_variant 0.25
aftB 4268566 p.Ser91Ala missense_variant 1.0
ethA 4328459 c.-986A>G upstream_gene_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0