TB-Profiler result

Run: SRR22528576
Summary

Run ID: SRR22528576

Sample name:

Date: 04-04-2023 04:19:08

Number of reads: 2386701

Percentage reads mapped: 99.66

Strain: lineage4.1.1

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
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 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761004 p.Thr400Ala missense_variant 0.61 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin
embB 4247431 p.Met306Ile missense_variant 1.0 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 5858 p.Asn207Asp missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.23
mshA 576482 p.Val379Leu missense_variant 0.12
rpoC 764817 p.Val483Gly missense_variant 0.23
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765588 c.2220_2222delGCG disruptive_inframe_deletion 0.23
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 0.98
tlyA 1917792 c.-148G>A upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290113 c.-872G>A upstream_gene_variant 1.0
pepQ 2860077 c.342G>A synonymous_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.17
ribD 2987553 p.Arg239Cys missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.98
fbiD 3339734 p.Ala206Gly missense_variant 0.31
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
embB 4246584 p.Arg24Pro missense_variant 0.55
embB 4247028 p.Leu172Arg missense_variant 0.2
embB 4249408 c.2895G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407946 p.Leu86His missense_variant 1.0