TB-Profiler result

Run: ERR10680155
Summary

Run ID: ERR10680155

Sample name:

Date: 31-03-2023 10:39:02

Number of reads: 2615532

Percentage reads mapped: 99.6

Strain: lineage4.8

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288718 p.Met175Arg missense_variant 0.35 pyrazinamide
pncA 2289054 c.187delG frameshift_variant 0.17 pyrazinamide
embB 4247429 p.Met306Val 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.26
mshA 576113 p.Arg256Gly missense_variant 0.32
rpoB 762475 p.Gly890Val missense_variant 1.0
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 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746529 p.Ala357Val missense_variant 0.98
fbiD 3339734 p.Ala206Gly missense_variant 0.86
fbiD 3339749 p.Val211Gly missense_variant 0.38
whiB7 3568428 c.252A>G synonymous_variant 0.15
rpoA 3878641 c.-134C>G upstream_gene_variant 0.18
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246529 p.Ser6Arg missense_variant 0.33
embB 4247028 p.Leu172Arg missense_variant 0.23
ubiA 4269116 p.Arg240Cys missense_variant 0.15
ethA 4326153 p.Arg441Cys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0