TB-Profiler result

Run: SRR22528575
Summary

Run ID: SRR22528575

Sample name:

Date: 04-04-2023 04:19:06

Number of reads: 616997

Percentage reads mapped: 99.79

Strain: lineage4.3.4.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247645 p.Glu378Lys missense_variant 0.14 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
gyrB 7197 p.Gly653Asp missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8091 p.Arg264Cys missense_variant 0.18
gyrA 8558 c.1257C>T synonymous_variant 0.15
gyrA 8566 p.Ile422Asn missense_variant 0.14
gyrA 8674 p.Ile458Thr missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491299 p.Tyr173His missense_variant 0.14
fgd1 491504 p.Leu241Pro missense_variant 0.18
mshA 576123 p.Leu259Arg missense_variant 0.21
rpoB 760204 p.Phe133Ser missense_variant 0.11
rpoB 762923 c.3118delA frameshift_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766458 p.Arg1030Pro missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776078 c.2403C>T synonymous_variant 0.13
mmpL5 777416 c.1064delC frameshift_variant 0.12
mmpL5 778255 p.Lys76Glu missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461008 c.-37G>A upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475029 n.1377delG non_coding_transcript_exon_variant 0.14
rrl 1475299 n.1642G>A non_coding_transcript_exon_variant 0.29
rpsA 1834043 p.Glu168Lys missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 0.91
ndh 2102455 c.588G>A synonymous_variant 0.18
katG 2154975 c.1137C>T synonymous_variant 0.29
PPE35 2167836 p.Gly926Ala missense_variant 0.22
PPE35 2168918 c.1695T>C synonymous_variant 0.15
PPE35 2169321 p.Leu431Trp missense_variant 0.15
PPE35 2169448 p.Phe389Ile missense_variant 0.2
PPE35 2170803 c.-191G>A upstream_gene_variant 1.0
Rv1979c 2223123 c.42G>A synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290200 c.-959A>T upstream_gene_variant 0.2
ahpC 2726598 p.Phe136Ile missense_variant 0.13
Rv2752c 3065092 p.Gln367Leu missense_variant 0.15
Rv2752c 3066074 p.Leu40Val missense_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039797 p.Asp303Gly missense_variant 0.11
clpC1 4040387 c.318A>G synonymous_variant 0.12
embC 4240372 c.510A>G synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247635 c.1122G>A synonymous_variant 0.15
ethR 4328053 p.His169Tyr missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407539 p.Gly222Arg missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0