TB-Profiler result

Run: ERR11068350
Summary

Run ID: ERR11068350

Sample name:

Date: 06-04-2023 09:20:30

Number of reads: 3323719

Percentage reads mapped: 99.62

Strain: lineage4.8;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 0.37
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.61
lineage4.1.2 Euro-American T;H None 0.36
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.37
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 2155168 p.Ser315Thr missense_variant 0.48 isoniazid
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 0.35
gyrA 9304 p.Gly668Asp missense_variant 0.34
fgd1 491591 p.Lys270Met missense_variant 0.4
mshA 575679 p.Asn111Ser missense_variant 0.32
mshA 576108 p.Ala254Gly missense_variant 0.21
rpoB 760106 c.300G>A synonymous_variant 0.39
rpoB 760115 c.309C>T synonymous_variant 0.37
rpoC 765150 p.Gly594Glu missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
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 0.68
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2222895 c.270C>A synonymous_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.32
ald 3086788 c.-32T>C upstream_gene_variant 0.37
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.35
rpoA 3878641 c.-134C>G upstream_gene_variant 0.2
clpC1 4039886 c.819C>T synonymous_variant 0.57
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.48
embB 4246584 p.Arg24Pro missense_variant 0.18
embB 4247024 p.Pro171Ala missense_variant 0.36
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408085 p.Glu40Gln missense_variant 0.29