TB-Profiler result

Run: ERR4195506
Summary

Run ID: ERR4195506

Sample name:

Date: 01-04-2023 05:20:37

Number of reads: 656799

Percentage reads mapped: 99.73

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 2154730 p.Gln461Pro missense_variant 0.14 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 9424 p.Asp708Ala missense_variant 1.0
rpoB 761152 p.Leu449Gln missense_variant 0.12
rpoC 766813 c.3444G>A synonymous_variant 0.95
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777128 c.1353A>G synonymous_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303749 c.819G>T synonymous_variant 0.9
fbiC 1304969 p.Leu680Pro missense_variant 0.13
fbiC 1305380 p.Ser817Leu missense_variant 0.11
atpE 1460992 c.-53A>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673357 c.-83G>A upstream_gene_variant 0.15
fabG1 1673359 c.-81T>C upstream_gene_variant 0.15
fabG1 1673361 c.-79C>G upstream_gene_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.25
rpsA 1834903 c.1362A>T synonymous_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155922 p.Tyr64Asp missense_variant 0.75
PPE35 2169902 c.711G>C synonymous_variant 0.13
PPE35 2169910 p.Asn235Tyr missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.12
PPE35 2170053 p.Thr187Ser missense_variant 0.12
PPE35 2170157 p.Ala152Ser missense_variant 0.16
PPE35 2170454 c.159C>G synonymous_variant 0.12
PPE35 2170457 c.156G>C synonymous_variant 0.12
PPE35 2170460 c.153G>A synonymous_variant 0.13
PPE35 2170465 p.Ala50Ser missense_variant 0.14
PPE35 2170472 c.141G>A synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289428 c.-187A>G upstream_gene_variant 0.12
kasA 2519089 c.975C>T synonymous_variant 0.22
Rv3236c 3612592 c.525C>T synonymous_variant 0.15
alr 3840764 c.657G>C synonymous_variant 1.0
rpoA 3878531 c.-24A>T upstream_gene_variant 0.22
clpC1 4039645 p.His354Asp missense_variant 0.17
clpC1 4039654 p.Thr351Ser missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269826 p.Glu3Val missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408342 c.-140C>G upstream_gene_variant 1.0
gid 4408469 c.-267T>A upstream_gene_variant 0.12
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0