TB-Profiler result

Run: SRR6207280
Summary

Run ID: SRR6207280

Sample name:

Date: 02-08-2023 15:06:57

Number of reads: NA

Percentage reads mapped: NA

Strain: lineage4.4.1.1

Drug-resistance: MDR-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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans 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 761095 p.Leu430Pro missense_variant 1.0 rifampicin
rpoB 761284 p.Ser493Leu missense_variant 0.31 rifampicin
fabG1 1673432 c.-8T>C upstream_gene_variant 1.0 isoniazid, ethionamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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 6691 p.Lys484Asn missense_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7885 p.Arg195His missense_variant 0.12
gyrA 8709 p.Ala470Thr missense_variant 0.1
gyrA 9138 p.Gln613Glu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576378 p.Asp344Gly missense_variant 0.22
ccsA 620173 p.Val95Ile missense_variant 0.22
rpoB 760315 p.Val170Ala missense_variant 0.47
rpoB 760591 p.Val262Ala missense_variant 1.0
rpoC 767139 p.Leu1257Pro missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777416 c.1065G>T synonymous_variant 1.0
mmpL5 778438 p.Pro15Thr missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407378 c.-38C>A upstream_gene_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471997 n.152T>G non_coding_transcript_exon_variant 0.11
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.13
rrs 1472189 n.344C>A non_coding_transcript_exon_variant 0.18
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.13
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.13
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.13
rrl 1474156 n.499G>T non_coding_transcript_exon_variant 0.2
rrl 1475426 n.1769C>T non_coding_transcript_exon_variant 0.12
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.2
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.2
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.25
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.25
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.25
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102083 c.960G>T synonymous_variant 0.11
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2154377 p.Thr579Ala missense_variant 1.0
PPE35 2168479 p.Thr712Pro missense_variant 1.0
PPE35 2169664 p.Gly317Cys missense_variant 0.11
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519055 p.Ala314Glu missense_variant 0.15
eis 2715384 c.-52C>T upstream_gene_variant 0.14
folC 2747125 p.Met158Ile missense_variant 0.18
pepQ 2859543 p.His292Gln missense_variant 0.15
pepQ 2860127 p.Glu98Gln missense_variant 0.15
ribD 2987289 p.Asp151Tyr missense_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475304 p.Ala433Asp missense_variant 0.15
whiB7 3568779 c.-100T>C upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiB 3642078 p.Pro182Thr missense_variant 0.22
alr 3840723 p.His233Arg missense_variant 0.12
rpoA 3878521 c.-14G>T upstream_gene_variant 0.29
ddn 3987219 c.376T>C synonymous_variant 0.12
clpC1 4039348 p.Arg453Gly missense_variant 0.11
clpC1 4039748 c.957G>A synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267119 c.1717delG frameshift_variant 0.11
aftB 4269021 c.-185C>T upstream_gene_variant 0.12
whiB6 4338209 p.Pro105Ser missense_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0