TB-Profiler result

Run: SRR3732654
Summary

Run ID: SRR3732654

Sample name:

Date: 04-04-2023 05:37:11

Number of reads: 486667

Percentage reads mapped: 99.3

Strain: lineage4

Drug-resistance: RR-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
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
rpoB 761108 p.Met434Ile missense_variant 1.0 rifampicin
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 5161 c.-79C>A upstream_gene_variant 0.33
gyrB 6347 p.Gln370Lys missense_variant 0.4
gyrB 7079 p.Gly614Cys missense_variant 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7380 p.Ser27Cys missense_variant 0.4
gyrA 7585 p.Ser95Thr missense_variant 1.0
fgd1 491182 p.Glu134* stop_gained 0.29
fgd1 491385 p.Glu201Asp missense_variant 0.4
rpoB 760982 c.1176G>T synonymous_variant 0.33
rpoC 762770 c.-600C>A upstream_gene_variant 0.67
rpoC 762965 c.-405T>C upstream_gene_variant 0.25
rpoC 763676 p.His103Asn missense_variant 0.22
rpoC 763733 p.Pro122Thr missense_variant 0.4
rpoC 764258 p.Lys297Glu missense_variant 0.5
rpoC 764541 p.Val391Gly missense_variant 0.67
rpoC 764543 p.Thr392Asp missense_variant 0.67
rpoC 765628 c.2259G>T synonymous_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781403 c.-157G>T upstream_gene_variant 0.29
rpsL 781709 c.150G>T synonymous_variant 0.25
embR 1416758 p.Leu197Pro missense_variant 0.33
embR 1417248 c.99delC frameshift_variant 0.67
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471779 n.-67T>A upstream_gene_variant 0.29
rrs 1472102 n.257G>T non_coding_transcript_exon_variant 0.5
rrl 1476394 n.2737C>A non_coding_transcript_exon_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102695 c.348C>A synonymous_variant 0.67
PPE35 2167968 p.Pro882Gln missense_variant 0.4
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517996 c.-119T>C upstream_gene_variant 0.5
ahpC 2726285 c.93C>T synonymous_variant 0.67
folC 2747028 p.Val191Ile missense_variant 0.22
pepQ 2859749 p.Ala224Thr missense_variant 0.5
thyA 3073704 c.768G>A synonymous_variant 1.0
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3475155 c.1149C>A synonymous_variant 0.5
fprA 3475237 p.Ala411Thr missense_variant 0.25
fprA 3475251 c.1245G>T synonymous_variant 0.25
fprA 3475300 p.Ala432Leu missense_variant 0.25
whiB7 3568467 p.Phe71Leu missense_variant 0.33
Rv3236c 3612511 p.Trp202Cys missense_variant 0.5
fbiA 3640670 p.Ala43Asp missense_variant 0.33
alr 3841419 p.Val1Glu missense_variant 0.29
rpoA 3878384 p.Leu42Met missense_variant 0.4
ddn 3987011 c.168C>T synonymous_variant 1.0
clpC1 4038668 c.2037G>T synonymous_variant 0.33
clpC1 4039783 p.Leu308Met missense_variant 0.25
clpC1 4040553 p.Ser51* stop_gained 0.14
panD 4043879 c.403C>A synonymous_variant 0.67
panD 4044107 p.Ala59Thr missense_variant 0.29
embC 4239881 p.Pro7Thr missense_variant 0.5
embC 4240776 p.Glu305Gly missense_variant 0.29
embC 4241866 c.2004G>T synonymous_variant 0.5
embC 4241921 p.Gly687Trp missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244531 c.1299G>T synonymous_variant 0.4
embB 4248028 c.1515C>A synonymous_variant 0.67
embB 4248432 p.Trp640Leu missense_variant 0.67
embB 4248799 c.2286T>C synonymous_variant 0.25
embB 4249086 p.Leu858Pro missense_variant 0.67
embB 4249633 c.3120C>A synonymous_variant 0.33
ethA 4326208 c.1266G>T synonymous_variant 1.0
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4326999 p.Gly159Trp missense_variant 0.25
ethR 4327444 c.-105C>A upstream_gene_variant 0.33
ethA 4328004 c.-531C>T upstream_gene_variant 1.0