TB-Profiler result

Run: ERR4830743
Summary

Run ID: ERR4830743

Sample name:

Date: 01-04-2023 20:25:28

Number of reads: 2897391

Percentage reads mapped: 99.11

Strain: lineage4.1.2

Drug-resistance: Pre-XDR-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 1.0
lineage4.1.2 Euro-American T;H None 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
gyrA 7572 p.Ser91Pro missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Asp missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embA 4243222 c.-11C>A upstream_gene_variant 1.0 ethambutol
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4327409 p.His22Pro missense_variant 1.0 ethionamide
ethR 4327876 p.Phe110Leu missense_variant 1.0 ethionamide
gid 4408087 c.115delC frameshift_variant 1.0 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800889 c.81C>A synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.12
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.12
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.11
rrs 1472431 n.586G>A non_coding_transcript_exon_variant 0.13
rrl 1474162 n.505C>T non_coding_transcript_exon_variant 0.15
rrl 1475050 n.1393A>G non_coding_transcript_exon_variant 0.22
rrl 1475859 n.2202G>A non_coding_transcript_exon_variant 0.14
rrl 1475878 n.2221T>C non_coding_transcript_exon_variant 0.2
rrl 1475979 n.2322T>C non_coding_transcript_exon_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103234 c.-192G>T upstream_gene_variant 1.0
PPE35 2168303 c.2310G>T synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288944 p.Thr100Pro missense_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840263 c.1158C>T synonymous_variant 1.0
alr 3841362 p.Thr20Met missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.31
aftB 4267091 c.1746C>A synonymous_variant 1.0
ethA 4328412 c.-939G>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0