TB-Profiler result

Run: SRR4033420

Summary

Run ID: SRR4033420

Sample name:

Date: 04-04-2023 06:04:57

Number of reads: 962027

Percentage reads mapped: 98.9

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 0.99
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 5331 p.Gly31Asp missense_variant 0.11
gyrB 5520 p.Pro94Leu missense_variant 1.0
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 7894 p.Ala198Val missense_variant 0.22
gyrA 8358 p.Pro353Ser missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491052 c.270C>T synonymous_variant 0.11
mshA 575935 c.588G>A synonymous_variant 0.12
mshA 576655 c.1308G>A synonymous_variant 0.11
rpoB 761298 p.Ala498Thr missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765434 p.His689Tyr missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801355 p.His183Asn missense_variant 0.12
atpE 1460855 c.-189delC upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1475518 n.1863delG non_coding_transcript_exon_variant 0.12
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.22
inhA 1674952 p.Pro251Ala missense_variant 0.15
tlyA 1917815 c.-125C>A upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103219 c.-177G>T upstream_gene_variant 0.11
katG 2154018 c.2094C>T synonymous_variant 0.12
katG 2154157 p.Ser652* stop_gained 0.11
katG 2154218 p.Arg632Ser missense_variant 0.12
katG 2155703 p.Asp137Asn missense_variant 0.11
katG 2155752 c.360C>T synonymous_variant 0.12
katG 2156260 c.-149C>A upstream_gene_variant 0.12
PPE35 2168040 p.Ala858Asp missense_variant 0.14
PPE35 2169114 p.Ala500Val missense_variant 0.13
PPE35 2169320 p.Leu431Phe missense_variant 0.35
Rv1979c 2222803 p.Ala121Val missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474091 p.Thr29Ala missense_variant 0.11
Rv3236c 3612549 p.Ala190Pro missense_variant 0.17
fbiA 3641095 p.Phe185Val missense_variant 0.25
fbiB 3642857 c.1323C>T synonymous_variant 0.11
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.22
clpC1 4040706 c.-2C>T upstream_gene_variant 0.15
embC 4239842 c.-21C>A upstream_gene_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.18
embA 4245299 c.2068_2069delCT frameshift_variant 0.14
embA 4246240 p.Pro1003Leu missense_variant 0.18
embB 4247414 p.Gly301Arg missense_variant 0.14
embB 4249275 p.Leu921Pro missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0