TB-Profiler result

Run: ERR11081939
Summary

Run ID: ERR11081939

Sample name:

Date: 09-04-2023 16:58:46

Number of reads: 2137143

Percentage reads mapped: 99.53

Strain: lineage4.2;lineage3

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
lineage3 East-African-Indian CAS RD750 0.92
lineage4 Euro-American LAM;T;S;X;H None 0.09
lineage4.2 Euro-American H;T;LAM None 0.06
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 0.99 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.97 isoniazid
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 8056 p.Arg252Leu missense_variant 0.93
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.91
mshA 576108 p.Ala254Gly missense_variant 0.13
mshA 576482 p.Val379Leu missense_variant 0.15
rpoB 759746 c.-61C>T upstream_gene_variant 0.93
rpoC 762434 c.-936T>G upstream_gene_variant 0.83
rpoC 763031 c.-339T>C upstream_gene_variant 0.86
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.89
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.93
PPE35 2167926 p.Leu896Ser missense_variant 0.93
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.93
pncA 2289365 c.-125delC upstream_gene_variant 0.9
ahpC 2726105 c.-88G>A upstream_gene_variant 0.93
pepQ 2860159 p.Ala87Gly missense_variant 0.27
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.5
fbiD 3339736 p.Thr207Pro missense_variant 0.4
fbiD 3339739 p.Ala208Pro missense_variant 0.4
fbiD 3339744 c.627A>C synonymous_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>C synonymous_variant 0.25
whiB7 3568428 c.252A>G synonymous_variant 0.46
rpoA 3878609 c.-102T>G upstream_gene_variant 0.29
embC 4242075 p.Arg738Gln missense_variant 0.93
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.32
ethA 4328212 c.-740delC upstream_gene_variant 0.85
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.88