TB-Profiler result

Run: SRR7516324
Summary

Run ID: SRR7516324

Sample name:

Date: 04-04-2023 19:23:21

Number of reads: 2300426

Percentage reads mapped: 99.66

Strain: lineage4.8;lineage2.2.1

Drug-resistance: MDR-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
lineage2 East-Asian Beijing RD105 0.09
lineage4 Euro-American LAM;T;S;X;H None 0.95
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.92
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.07
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
rpoB 761155 p.Ser450Leu missense_variant 0.91 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.92 isoniazid
embB 4247730 p.Gly406Asp missense_variant 0.97 ethambutol
gid 4407896 p.Glu103* stop_gained 0.88 streptomycin
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
mshA 576108 p.Ala254Gly missense_variant 0.28
rpoB 761998 p.Leu731Pro missense_variant 0.88
rpoC 763031 c.-339T>C upstream_gene_variant 0.1
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 0.91
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.16
PPE35 2167926 p.Leu896Ser missense_variant 0.13
PPE35 2168149 p.Pro822Ser missense_variant 0.96
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.18
clpC1 4039729 p.Asp326Asn missense_variant 0.84
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.22
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0