TB-Profiler result

Run: ERR2653110
Summary

Run ID: ERR2653110

Sample name:

Date: 31-03-2023 22:31:51

Number of reads: 576394

Percentage reads mapped: 99.45

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.99
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.99
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 0.96 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288730 p.Ala171Glu missense_variant 1.0 pyrazinamide
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
gyrB 6804 p.Leu522Pro missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776086 p.Val799Ile missense_variant 0.13
mmpL5 778071 p.Thr137Asn missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801304 c.497delT frameshift_variant 0.12
fbiC 1303016 p.Val29Gly missense_variant 0.21
fbiC 1304196 c.1266C>T synonymous_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.1
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102710 c.333C>A synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
pepQ 2859601 c.817delG frameshift_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339180 c.63G>C synonymous_variant 0.1
fbiD 3339741 c.624G>T synonymous_variant 0.12
fbiD 3339744 c.627A>C synonymous_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039501 p.Leu402Val missense_variant 1.0
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.12
embB 4246548 p.Pro12Gln missense_variant 0.13
embB 4246555 c.42G>C synonymous_variant 0.13
embB 4246556 p.Ala15Pro missense_variant 0.13
embB 4246563 p.Leu17Trp missense_variant 0.14
embB 4246567 c.54G>T synonymous_variant 0.15
embB 4247783 p.Arg424Trp missense_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0