TB-Profiler result

Run: ERR2229422
Summary

Run ID: ERR2229422

Sample name:

Date: 31-03-2023 17:10:28

Number of reads: 192945

Percentage reads mapped: 99.28

Strain: lineage4.8

Drug-resistance: HR-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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
katG 2154746 c.1365dupT frameshift_variant 0.33 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
gyrB 5630 p.Leu131Ile missense_variant 0.21
gyrB 6162 p.Ile308Asn missense_variant 0.4
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 491771 p.Pro330Leu missense_variant 0.29
rpoB 759614 c.-193C>T upstream_gene_variant 0.67
rpoB 761440 p.Asp545Gly missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775726 c.2755C>T synonymous_variant 0.5
mmpL5 775727 c.2754C>G synonymous_variant 0.5
mmpL5 775736 c.2745C>G synonymous_variant 0.4
mmpL5 775741 c.2740C>T synonymous_variant 0.4
mmpL5 775742 c.2739C>T synonymous_variant 0.4
mmpL5 777134 p.Met449Ile missense_variant 0.5
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800694 c.-115C>T upstream_gene_variant 0.2
fbiC 1303148 p.Ala73Asp missense_variant 0.67
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.75
rpsA 1834583 c.1045_1047delATC conservative_inframe_deletion 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154499 p.Val538Ala missense_variant 0.29
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169302 p.Met437Phe missense_variant 0.4
PPE35 2169884 c.729T>C synonymous_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726617 p.Asn142Thr missense_variant 0.25
folC 2746441 c.1158C>T synonymous_variant 0.67
thyX 3067909 p.Ala13Thr missense_variant 0.29
thyA 3074395 p.Thr26Asn missense_variant 0.5
ald 3086776 c.-44G>A upstream_gene_variant 0.22
whiB7 3568800 c.-121C>T upstream_gene_variant 0.5
Rv3236c 3613303 c.-187C>T upstream_gene_variant 0.29
alr 3841546 c.-126C>A upstream_gene_variant 0.38
rpoA 3878093 p.Val139Ile missense_variant 0.33
clpC1 4040482 p.Ser75Thr missense_variant 0.33
embC 4242531 p.Arg890Gln missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0