TB-Profiler result

Run: SRR2101683

Summary

Run ID: SRR2101683

Sample name:

Date: 03-04-2023 23:51:32

Number of reads: 363777

Percentage reads mapped: 99.57

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
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 8699 c.1398A>G synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.21
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 764311 c.942C>A synonymous_variant 0.15
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765584 p.Pro739Ser missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775939 p.Ala848Thr missense_variant 0.22
mmpL5 779292 c.-812C>T upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303606 p.Lys226Glu missense_variant 0.1
Rv1258c 1407350 c.-10C>T upstream_gene_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474705 n.1048T>A non_coding_transcript_exon_variant 0.11
rrl 1476382 n.2725A>T non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918701 p.Lys254Asn missense_variant 0.17
katG 2155754 p.Gly120Cys missense_variant 0.13
PPE35 2169228 p.Leu462Pro missense_variant 0.12
PPE35 2170424 c.189G>T synonymous_variant 0.29
Rv1979c 2222512 p.Phe218Cys missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
folC 2747424 p.Ser59Pro missense_variant 0.17
pepQ 2859862 p.Asp186Val missense_variant 0.14
ribD 2987547 c.709C>A synonymous_variant 0.13
Rv2752c 3065148 c.1044C>A synonymous_variant 0.1
Rv2752c 3065456 p.Gln246* stop_gained 0.12
thyX 3067229 c.717C>A synonymous_variant 0.13
thyX 3067274 c.672C>A synonymous_variant 0.17
thyA 3074198 p.Pro92Ser missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448490 c.-14A>G upstream_gene_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3877591 p.Leu306Pro missense_variant 0.18
clpC1 4039484 c.1221T>G synonymous_variant 0.29
clpC1 4039679 p.Phe342Leu missense_variant 0.12
embC 4240122 p.Pro87His missense_variant 0.12
embC 4240439 p.Phe193Leu missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243829 c.597C>A synonymous_variant 0.18
embA 4244090 p.Lys286Asn missense_variant 0.12
embA 4244393 c.1161G>T synonymous_variant 0.12
embA 4244505 p.Gly425Trp missense_variant 0.12
embA 4245817 p.Arg862Leu missense_variant 0.14
embB 4247010 p.Asp166Gly missense_variant 0.15
embB 4248971 p.Lys820Glu missense_variant 0.14
ubiA 4269310 p.Trp175Leu missense_variant 0.11
aftB 4269324 c.-488C>A upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0