TB-Profiler result

Run: ERR2516663
Summary

Run ID: ERR2516663

Sample name:

Date: 31-03-2023 21:39:59

Number of reads: 1866918

Percentage reads mapped: 99.62

Strain: lineage4.1.1.3

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
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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 7582 p.Asp94Gly missense_variant 0.23 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764948 p.Leu527Val missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289199 p.Glu15* stop_gained 1.0 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
ethA 4327159 c.314dupT frameshift_variant 1.0 ethionamide
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 8164 p.Ala288Asp missense_variant 0.75
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 776813 c.1668G>A synonymous_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302954 c.24G>A synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471861 n.16T>C non_coding_transcript_exon_variant 0.15
rrs 1471872 n.27T>A non_coding_transcript_exon_variant 0.14
rrs 1471947 n.102G>A non_coding_transcript_exon_variant 0.2
rrs 1472363 n.518G>A non_coding_transcript_exon_variant 0.29
rrs 1473279 n.1434G>T non_coding_transcript_exon_variant 0.18
rrl 1476785 n.3128A>G non_coding_transcript_exon_variant 0.17
rrl 1476795 n.3138A>G splice_region_variant&non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154678 c.1434G>C synonymous_variant 1.0
PPE35 2169405 p.Asn403Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726409 p.Asp73His missense_variant 1.0
ribD 2987307 p.Ala157Pro missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449437 c.936_942delCGCGGCG frameshift_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.13
embB 4249408 c.2895G>A synonymous_variant 0.98
embB 4249678 c.3165C>A synonymous_variant 1.0
ubiA 4269296 p.Met180Val missense_variant 1.0
gid 4407934 p.Leu90Arg missense_variant 1.0
whiB6 4337479 c.-219_*691del transcript_ablation 1.0