TB-Profiler result

Run: SRR6896355
Summary

Run ID: SRR6896355

Sample name:

Date: 04-04-2023 18:03:23

Number of reads: 384035

Percentage reads mapped: 99.78

Strain: lineage4.3.2.1

Drug-resistance: HR-TB

Download CSV Download TXT Download PDF Download JSON
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
katG 2155816 p.Gly99Glu missense_variant 0.2 isoniazid
panD 4043900 p.Ala128Ser missense_variant 0.12 pyrazinamide
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
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 9304 p.Gly668Asp missense_variant 1.0
mshA 576634 c.1287G>C synonymous_variant 0.13
rpoB 760569 p.Thr255Ala missense_variant 0.11
rpoB 761128 c.1326delG frameshift_variant 0.11
rpoB 761736 p.Ile644Val missense_variant 0.11
rpoC 762842 c.-528G>A upstream_gene_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303951 p.Asp341Tyr missense_variant 0.15
fbiC 1304109 c.1179C>G synonymous_variant 0.12
embR 1416734 c.613delG frameshift_variant 0.11
atpE 1461129 p.Gly29Arg missense_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 1474238 n.581G>T non_coding_transcript_exon_variant 0.11
rrl 1475201 n.1544G>C non_coding_transcript_exon_variant 0.25
rrl 1475551 n.1894T>C non_coding_transcript_exon_variant 0.14
rpsA 1833621 p.Asp27Gly missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167876 p.Gly913Cys missense_variant 0.12
Rv1979c 2222933 p.Ser78Pro missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289050 c.192T>C synonymous_variant 0.12
pncA 2289889 c.-648C>A upstream_gene_variant 0.17
pncA 2290188 c.-947A>G upstream_gene_variant 0.12
ribD 2987193 p.Ile119Val missense_variant 0.13
ribD 2987487 p.Pro217Ser missense_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074258 c.213dupG frameshift_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448974 c.471C>T synonymous_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878059 p.Val150Ala missense_variant 0.14
rpoA 3878450 p.Gln20* stop_gained 0.18
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040503 p.Gly68Ser missense_variant 0.12
embC 4239881 p.Pro7Thr missense_variant 0.33
embC 4240714 p.Trp284Cys missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245307 c.2077delG frameshift_variant 0.12
embB 4246490 c.-24G>A upstream_gene_variant 0.12
embB 4246776 p.Val88Ala missense_variant 0.15
aftB 4267634 c.1203G>T synonymous_variant 0.14
aftB 4267723 p.Val372Phe missense_variant 0.13
aftB 4268229 p.Ala203Val missense_variant 0.11
aftB 4268812 p.Ser9Pro missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0