TB-Profiler result

Run: SRR1173542
Summary

Run ID: SRR1173542

Sample name:

Date: 03-04-2023 03:27:12

Number of reads: 4742021

Percentage reads mapped: 95.63

Strain: lineage4.1.2

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
lineage4.1 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
rpoB 761139 p.His445Cys missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 0.98 pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
alr 3841409 p.Phe4Leu missense_variant 1.0 cycloserine
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326705 c.767_768delGG frameshift_variant 1.0 ethionamide
gid 4408100 c.102delG 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
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776858 c.1623C>T synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417140 p.Ala70Ser missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.12
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.13
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.12
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.13
rrl 1476353 n.2696G>A non_coding_transcript_exon_variant 0.13
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.12
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.11
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.15
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.15
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.13
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.14
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.14
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.12
fabG1 1673249 c.-191C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726121 c.-72C>T upstream_gene_variant 1.0
folC 2747022 p.Val193Ile missense_variant 1.0
thyA 3074073 p.Trp133* stop_gained 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448894 p.Tyr131Asp missense_variant 1.0
Rv3083 3449642 p.Asn380Ser missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474382 p.Val126Ile missense_variant 1.0
fbiA 3641164 p.Ile208Val missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
aftB 4268861 c.-25T>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338674 c.-153G>A upstream_gene_variant 0.99