TB-Profiler result

Run: SRR4034383
Summary

Run ID: SRR4034383

Sample name:

Date: 04-04-2023 06:45:32

Number of reads: 1322982

Percentage reads mapped: 99.53

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 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 2155058 p.Gln352* stop_gained 0.18 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 6636 p.Ser466Tyr missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 9177 p.Ala626Thr missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575369 p.Asp8Tyr missense_variant 0.13
rpoB 760062 p.Glu86* stop_gained 0.12
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760511 c.705G>T synonymous_variant 0.15
rpoB 760787 c.981G>T synonymous_variant 0.17
rpoB 761811 p.Phe669Leu missense_variant 0.11
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpS5 778564 p.Cys114* stop_gained 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801398 p.Ala197Glu missense_variant 0.11
atpE 1461275 c.231T>C synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918284 c.345C>T synonymous_variant 0.11
ndh 2102402 p.Leu214His missense_variant 0.11
katG 2156550 c.-439G>A upstream_gene_variant 0.11
PPE35 2170187 p.Glu142Asp missense_variant 0.22
Rv1979c 2222893 p.Gly91Asp missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518215 c.104delG frameshift_variant 0.12
kasA 2518868 p.Glu252* stop_gained 0.2
folC 2746223 p.Asp459Val missense_variant 0.22
pepQ 2860150 p.Ala90Val missense_variant 0.17
ribD 2987385 p.Ala183Thr missense_variant 0.11
Rv2752c 3065067 c.1124delA frameshift_variant 0.11
Rv2752c 3066172 p.Pro7Gln missense_variant 0.12
thyX 3067557 p.His130Leu missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
fbiB 3642269 c.735C>A synonymous_variant 0.12
rpoA 3878632 c.-125C>A upstream_gene_variant 0.2
rpoA 3878641 c.-134C>G upstream_gene_variant 0.18
rpoA 3878650 c.-143C>A upstream_gene_variant 0.11
clpC1 4040090 c.615T>C synonymous_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243301 c.69G>T synonymous_variant 0.11
embB 4246525 c.12C>T synonymous_variant 0.11
ethR 4328012 p.Ala155Val missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408045 p.Ala53Asp missense_variant 0.12