TB-Profiler result

Run: SRR14782762
Summary

Run ID: SRR14782762

Sample name:

Date: 03-04-2023 11:38:44

Number of reads: 9799099

Percentage reads mapped: 99.43

Strain: lineage4.8;lineage4.2.1

Drug-resistance: Pre-XDR-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
lineage4.2 Euro-American H;T;LAM None 0.16
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.85
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.16
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
gyrA 7581 p.Asp94Asn missense_variant 0.12 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.13 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.15 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.15 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.15 isoniazid
pncA 2288850 c.390_391dupGG frameshift_variant 0.16 pyrazinamide, pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.15 kanamycin
embB 4247402 p.Ser297Ala missense_variant 0.16 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 0.18
fgd1 491247 c.465C>T synonymous_variant 0.12
ccsA 619969 p.Val27Ile missense_variant 0.12
rpoC 764817 p.Val483Gly missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.14
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 0.85
fabG1 1673553 p.Asp38Glu missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 0.82
PPE35 2169879 p.Phe245Cys missense_variant 0.17
PPE35 2170065 p.Ala183Gly missense_variant 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.18
ald 3086742 c.-78A>C upstream_gene_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 0.15
ald 3087220 c.402dupC frameshift_variant 0.11
fbiD 3339734 p.Ala206Gly missense_variant 0.75
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.15
rpoA 3878641 c.-134C>G upstream_gene_variant 0.55
embC 4239930 p.Gly23Glu missense_variant 0.8
embC 4240409 p.Pro183Ala missense_variant 0.24
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246529 p.Ser6Arg missense_variant 0.18
embB 4246584 p.Arg24Pro missense_variant 0.14
embB 4249594 c.3081G>A synonymous_variant 0.15
ethA 4326632 p.His281Pro missense_variant 0.14
ethA 4328376 c.-903G>C upstream_gene_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0