TB-Profiler result

Run: ERR7801183

Summary

Run ID: ERR7801183

Sample name:

Date: 02-04-2023 05:58:08

Number of reads: 768440

Percentage reads mapped: 99.65

Strain: lineage4.3.4.2

Drug-resistance: Other


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
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.99
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
ethA 4327198 p.Tyr92* stop_gained 0.13 ethionamide
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 5303 p.Gly22Trp missense_variant 0.15
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrB 6725 p.Val496Leu missense_variant 0.2
gyrB 6922 c.1688delT frameshift_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7467 p.Leu56Ile missense_variant 0.15
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7851 p.Gly184Cys missense_variant 0.17
gyrA 8021 c.720C>A synonymous_variant 0.17
gyrA 8370 c.1069C>A synonymous_variant 0.15
gyrA 8650 p.Arg450His missense_variant 0.25
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620487 c.597C>A synonymous_variant 0.13
rpoB 760221 p.Gly139Ser missense_variant 0.17
rpoB 760721 c.915C>T synonymous_variant 0.17
rpoB 761450 p.Phe548Leu missense_variant 0.17
rpoB 761489 p.Glu561Asp missense_variant 0.18
rpoB 762257 c.2451C>A synonymous_variant 0.25
rpoB 762275 c.2469C>A synonymous_variant 0.18
rpoB 762333 p.Gly843Cys missense_variant 0.14
rpoB 762474 p.Gly890Cys missense_variant 0.15
rpoB 762661 p.Arg952Met missense_variant 0.15
rpoC 763915 c.546C>A synonymous_variant 0.15
rpoC 764008 p.Gln213His missense_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765428 p.Gln687* stop_gained 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777975 p.Val169Ala missense_variant 0.13
mmpR5 778331 c.-659C>T upstream_gene_variant 0.18
mmpL5 778365 p.Trp39* stop_gained 0.2
mmpR5 779151 p.Glu54Asp missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305061 p.Gly711Trp missense_variant 0.15
Rv1258c 1406600 p.Phe247Leu missense_variant 0.14
embR 1416873 p.Val159Ile missense_variant 0.14
atpE 1461275 c.231T>C synonymous_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471986 n.144dupG non_coding_transcript_exon_variant 0.18
rrs 1472186 n.341C>T non_coding_transcript_exon_variant 0.2
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.17
rrs 1473014 n.1169G>T non_coding_transcript_exon_variant 0.18
rrl 1474980 n.1323G>T non_coding_transcript_exon_variant 0.15
rrl 1475189 n.1532G>T non_coding_transcript_exon_variant 0.29
rrl 1476377 n.2720A>T non_coding_transcript_exon_variant 0.33
fabG1 1673473 p.Pro12Thr missense_variant 0.13
fabG1 1673551 p.Asp38Tyr missense_variant 0.29
fabG1 1673581 p.Gly48* stop_gained 0.17
inhA 1673811 c.-391G>T upstream_gene_variant 0.13
fabG1 1673889 p.Gln150His missense_variant 0.14
inhA 1674450 c.249G>T synonymous_variant 0.18
inhA 1674714 c.513C>A synonymous_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102302 c.741G>A synonymous_variant 0.18
katG 2156435 c.-324G>A upstream_gene_variant 0.17
PPE35 2167853 p.Phe920Leu missense_variant 0.22
PPE35 2168410 p.Thr735Ser missense_variant 0.2
PPE35 2168416 p.Gly733Trp missense_variant 0.22
PPE35 2170354 p.Ala87Ser missense_variant 0.14
PPE35 2170378 p.Ala79Ser missense_variant 0.15
Rv1979c 2222842 c.322delG frameshift_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290024 c.-783C>A upstream_gene_variant 0.13
kasA 2518216 p.Lys34Asn missense_variant 0.22
kasA 2518275 p.Trp54Leu missense_variant 0.33
kasA 2518288 c.174C>A synonymous_variant 0.33
kasA 2518409 p.Gly99Cys missense_variant 0.18
kasA 2518497 p.Leu128Pro missense_variant 0.22
ahpC 2726188 c.-5G>T upstream_gene_variant 0.14
ahpC 2726589 p.Arg133Ser missense_variant 0.18
pepQ 2859350 p.Gln357Glu missense_variant 0.11
Rv2752c 3064827 c.1365C>A synonymous_variant 0.15
Rv2752c 3065231 p.Gly321Trp missense_variant 0.22
Rv2752c 3065301 c.891C>A synonymous_variant 0.2
Rv2752c 3065328 p.Asp288Glu missense_variant 0.18
Rv2752c 3066162 c.30C>A synonymous_variant 0.13
Rv2752c 3067074 c.-883C>A upstream_gene_variant 0.15
thyX 3067480 p.Asp156Tyr missense_variant 0.17
thyX 3068071 c.-126C>A upstream_gene_variant 0.14
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087276 p.Gln153Lys missense_variant 0.13
ald 3087294 p.Leu159Met missense_variant 0.17
ald 3087485 c.666C>A synonymous_variant 0.17
Rv3083 3448898 p.Thr132Asn missense_variant 0.12
Rv3083 3449231 p.Gly243Val missense_variant 0.12
Rv3083 3449435 c.935delG frameshift_variant 0.11
Rv3083 3449531 p.Val343Ala missense_variant 0.13
Rv3083 3449562 c.1059G>T synonymous_variant 0.13
Rv3083 3449933 p.Pro477His missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474117 p.Asp37Glu missense_variant 0.13
fprA 3474627 p.Phe207Leu missense_variant 0.15
fprA 3474919 p.Lys305Gln missense_variant 0.14
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612127 c.990C>A synonymous_variant 0.18
Rv3236c 3612942 p.Ala59Ser missense_variant 0.14
fbiB 3641726 c.192C>A synonymous_variant 0.15
rpoA 3877476 c.1032C>A synonymous_variant 0.17
rpoA 3877555 p.Ser318* stop_gained 0.15
rpoA 3877593 c.915C>A synonymous_variant 0.13
rpoA 3877637 p.Gln291Lys missense_variant 0.2
rpoA 3877847 p.Leu221Met missense_variant 0.17
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038691 p.Asp672Tyr missense_variant 0.15
clpC1 4038740 c.1965G>T synonymous_variant 0.22
clpC1 4039267 p.Asp480Tyr missense_variant 0.2
clpC1 4039462 p.Met415Val missense_variant 0.22
clpC1 4039475 p.Met410Ile missense_variant 0.18
embC 4241222 p.Gly454Arg missense_variant 0.18
embA 4242313 c.-920C>T upstream_gene_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244216 c.984C>A synonymous_variant 0.22
embA 4244306 c.1074G>T synonymous_variant 0.2
embB 4248393 p.Ala627Glu missense_variant 0.14
embB 4248397 p.Phe628Leu missense_variant 0.14
embB 4248480 c.1967delT frameshift_variant 0.17
embB 4249399 c.2886G>T synonymous_variant 0.18
aftB 4267462 p.Gln459Lys missense_variant 0.14
aftB 4267786 p.Gly351Trp missense_variant 0.15
aftB 4268474 p.Gly121Val missense_variant 0.17
ethR 4326982 c.-567C>T upstream_gene_variant 0.17
ethA 4328019 c.-546G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407703 p.Ala167Asp missense_variant 0.18
gid 4407734 p.Gly157Trp missense_variant 0.17
gid 4408071 c.132A>G synonymous_variant 0.15
gid 4408156 p.Leu16Arg missense_variant 0.94