TB-Profiler result

Run: ERR4819778
Summary

Run ID: ERR4819778

Sample name:

Date: 01-04-2023 16:18:01

Number of reads: 1271066

Percentage reads mapped: 99.72

Strain: lineage4.8

Drug-resistance: Other

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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
gid 4408087 c.115delC 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
gyrB 5760 p.Trp174* stop_gained 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576347 p.Thr334Ala missense_variant 1.0
ccsA 620544 c.654G>T synonymous_variant 0.12
rpoB 760698 p.Lys298Glu missense_variant 0.18
rpoB 762110 c.2304G>A synonymous_variant 0.2
rpoB 762653 p.Trp949* stop_gained 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776502 p.Glu660Gly missense_variant 0.13
mmpL5 776568 p.Met638Lys missense_variant 0.11
mmpL5 776601 p.Leu627Pro missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673502 c.-700C>A upstream_gene_variant 0.2
rpsA 1834102 c.561T>A synonymous_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103208 c.-166G>T upstream_gene_variant 0.12
katG 2154122 p.Met664Val missense_variant 0.11
katG 2154387 c.1725G>C synonymous_variant 0.12
PPE35 2168198 c.2415G>A synonymous_variant 0.22
PPE35 2169603 p.Gly337Asp missense_variant 0.13
PPE35 2169610 p.Gly335Cys missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290053 c.-812A>G upstream_gene_variant 0.13
pncA 2290132 c.-891C>T upstream_gene_variant 1.0
kasA 2519235 p.Glu374Gly missense_variant 0.13
pepQ 2859654 c.764delA frameshift_variant 0.12
Rv2752c 3064569 c.1623G>T synonymous_variant 0.12
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
embC 4240367 p.Val169Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245320 c.2088C>T synonymous_variant 1.0
ethA 4326144 p.Asp444Tyr missense_variant 0.13
ethA 4326972 p.Pro168Ser missense_variant 0.13
ethA 4327839 c.-366G>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0