TB-Profiler result

Run: SRR6896384

Summary

Run ID: SRR6896384

Sample name:

Date: 04-04-2023 18:04:26

Number of reads: 650988

Percentage reads mapped: 99.55

Strain: lineage4.3.2.1

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 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
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 5520 p.Pro94Leu missense_variant 1.0
gyrB 5757 p.Phe173Ser missense_variant 0.11
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8443 p.Leu381Pro missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491393 p.Thr204Ile missense_variant 0.1
fgd1 491544 p.Leu254Phe missense_variant 0.13
rpoB 759615 c.-192A>C upstream_gene_variant 0.17
rpoB 762623 p.Lys939Asn missense_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765719 p.Glu784Lys missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778811 p.Phe32Ser missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1474901 n.1244A>G non_coding_transcript_exon_variant 0.12
rrl 1476601 n.2944G>T non_coding_transcript_exon_variant 0.13
inhA 1674286 c.88delC frameshift_variant 0.11
inhA 1674834 c.633C>T synonymous_variant 0.87
rpsA 1833414 c.-127delT upstream_gene_variant 0.14
rpsA 1833603 p.Asp21Gly missense_variant 0.97
rpsA 1834940 p.Asp467Tyr missense_variant 0.14
tlyA 1917809 c.-131G>A upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156487 c.-376G>A upstream_gene_variant 0.12
PPE35 2169725 c.888T>C synonymous_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223337 c.-173C>T upstream_gene_variant 0.11
pncA 2289572 c.-331C>A upstream_gene_variant 0.14
eis 2715072 c.261G>T synonymous_variant 0.12
pepQ 2859919 p.Arg167Leu missense_variant 0.13
pepQ 2860030 p.Ser130* stop_gained 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087614 c.795G>A synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474159 c.153C>A synonymous_variant 0.13
fprA 3474191 p.Ser62* stop_gained 0.12
Rv3236c 3612129 p.Leu330Ile missense_variant 0.14
Rv3236c 3612511 p.Trp202Cys missense_variant 0.18
Rv3236c 3612929 p.Pro63His missense_variant 0.13
fbiA 3640383 c.-160_-159insT upstream_gene_variant 1.0
fbiB 3642075 p.Asp181Tyr missense_variant 0.13
fbiB 3642771 p.Asp413Asn missense_variant 0.15
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242191 p.Leu777Met missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243160 c.-73C>T upstream_gene_variant 1.0
embB 4245695 c.-819C>A upstream_gene_variant 0.12
embA 4245700 p.Gly823Ala missense_variant 0.12
aftB 4268641 c.196C>T synonymous_variant 0.15
ethA 4326995 p.Pro160Leu missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0