TB-Profiler result

Run: ERR3588247
Summary

Run ID: ERR3588247

Sample name:

Date: 01-04-2023 02:37:32

Number of reads: 72495

Percentage reads mapped: 94.26

Strain: lineage4.9;lineage4.3

Drug-resistance: Sensitive

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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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.13
lineage4.9 Euro-American (H37Rv-like) T1 None 0.95
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
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 5191 c.-49G>T upstream_gene_variant 0.5
gyrB 5450 p.Glu71Lys missense_variant 0.67
gyrB 5723 p.Ala162Ser missense_variant 1.0
gyrB 5998 p.Tyr253* stop_gained 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 575240 c.-108G>A upstream_gene_variant 1.0
rpoB 760551 p.Ser249Ala missense_variant 0.5
rpoC 763232 c.-138C>T upstream_gene_variant 0.2
rpoB 763264 p.Ala1153Glu missense_variant 0.29
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766265 p.Leu966Met missense_variant 0.67
mmpL5 775984 p.Trp833Arg missense_variant 0.67
mmpL5 776477 c.2004G>A synonymous_variant 0.5
mmpL5 777386 c.1095C>A synonymous_variant 1.0
mmpL5 777511 p.Leu324Met missense_variant 0.67
mmpR5 779474 p.Gly162Glu missense_variant 0.29
fbiC 1303251 p.Phe107Leu missense_variant 0.67
Rv1258c 1406622 p.Leu240Pro missense_variant 0.5
embR 1416361 c.987C>T synonymous_variant 0.33
embR 1416451 c.897C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472282 n.437T>G non_coding_transcript_exon_variant 0.4
rrs 1472377 n.532G>T non_coding_transcript_exon_variant 0.29
ndh 2102387 p.Ala219Val missense_variant 0.5
ndh 2102797 c.246C>A synonymous_variant 1.0
ndh 2102820 p.Val75Leu missense_variant 0.5
ndh 2103207 c.-165C>A upstream_gene_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
kasA 2519255 p.Asp381Tyr missense_variant 1.0
ahpC 2726100 c.-93G>A upstream_gene_variant 0.4
ahpC 2726676 c.484C>T synonymous_variant 0.5
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074039 p.Pro145Ala missense_variant 0.33
thyA 3074473 c.-2T>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087663 p.Thr282Ala missense_variant 1.0
fbiA 3640353 c.-190G>A upstream_gene_variant 0.33
alr 3840604 p.Pro273Thr missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038455 c.2250G>A synonymous_variant 0.4
clpC1 4039007 c.1698G>T synonymous_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243755 p.Thr175Pro missense_variant 0.5
embB 4248987 p.Gly825Val missense_variant 0.5
ethA 4326142 p.Asp444Glu missense_variant 0.38
ethR 4327597 p.Thr17Ala missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0