TB-Profiler result

Run: ERR6336751
Summary

Run ID: ERR6336751

Sample name:

Date: 02-04-2023 02:02:07

Number of reads: 1728343

Percentage reads mapped: 99.37

Strain: lineage4.3.4.1

Drug-resistance: Other

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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
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 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
embB 4247919 p.Arg469Pro missense_variant 0.15 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7932 p.Asp211Tyr missense_variant 0.2
gyrA 8529 p.Ala410Thr missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491110 p.Ala110Thr missense_variant 0.12
fgd1 491151 c.369G>A synonymous_variant 0.15
mshA 576108 p.Ala254Gly missense_variant 0.22
mshA 576419 p.Val358Phe missense_variant 0.12
mshA 576613 c.1266A>G synonymous_variant 0.14
ccsA 619793 c.-98G>A upstream_gene_variant 0.13
rpoB 761261 c.1458delC frameshift_variant 0.11
rpoB 762213 p.Lys803Glu missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777990 p.Glu164Gly missense_variant 0.18
mmpL5 778632 c.-152T>C upstream_gene_variant 0.14
mmpR5 779365 p.Gly126Arg missense_variant 0.17
mmpR5 779372 p.Ala128Val missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303749 c.819G>T synonymous_variant 1.0
fbiC 1304065 p.Ala379Thr missense_variant 0.25
fbiC 1304458 p.Thr510Ala missense_variant 0.15
embR 1416557 p.Lys264Val missense_variant 0.13
embR 1416976 p.His124Gln missense_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.1
inhA 1674332 p.Leu44Pro missense_variant 0.12
rpsA 1833990 p.Ala150Val missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101715 p.Glu443Gly missense_variant 0.11
katG 2155239 c.873T>A synonymous_variant 0.12
katG 2155360 p.Thr251Arg missense_variant 0.12
katG 2156491 c.-380C>T upstream_gene_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726323 p.Pro44Arg missense_variant 1.0
folC 2746309 c.1290G>A synonymous_variant 0.2
pepQ 2860159 p.Ala87Gly missense_variant 0.33
ribD 2987463 p.Asp209Asn missense_variant 0.12
ribD 2987494 p.Val219Ala missense_variant 0.12
Rv2752c 3064820 p.Gly458Ser missense_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087224 c.405A>G synonymous_variant 0.11
ald 3087932 c.1114delT frameshift_variant&stop_lost&splice_region_variant 0.25
fbiD 3339734 p.Ala206Gly missense_variant 0.4
Rv3083 3448874 p.Ala124Val missense_variant 0.2
Rv3083 3449298 c.796delC frameshift_variant 0.11
Rv3083 3449303 p.Arg267Gln missense_variant 0.12
Rv3083 3449738 p.His412Arg missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474076 p.Lys24Gln missense_variant 0.12
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612416 p.Glu234Ala missense_variant 0.17
fbiB 3641985 p.Thr151Ala missense_variant 0.22
fbiB 3642046 p.Ala171Gly missense_variant 0.12
fbiB 3642086 c.552C>T synonymous_variant 0.12
fbiB 3642269 c.735C>T synonymous_variant 0.29
rpoA 3877824 p.Glu228Asp missense_variant 0.12
rpoA 3878558 c.-51A>G upstream_gene_variant 0.12
rpoA 3878562 c.-55C>G upstream_gene_variant 0.13
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040242 p.Thr155Pro missense_variant 0.18
embC 4240411 c.549G>C synonymous_variant 0.4
embA 4242493 c.-740G>C upstream_gene_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242702 p.Ala947Val missense_variant 0.15
embC 4242705 p.Asp948Gly missense_variant 0.17
embC 4242762 p.Arg967Gln missense_variant 0.12
embA 4243928 c.696C>A synonymous_variant 0.2
embA 4244184 p.Ser318Arg missense_variant 0.12
embA 4244194 p.Gly321Ala missense_variant 0.12
embA 4245745 p.Pro838Arg missense_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.25
embB 4246548 p.Pro12Gln missense_variant 0.23
embB 4246574 p.Ala21Thr missense_variant 0.15
embB 4246694 p.Arg61Gly missense_variant 0.15
embB 4247902 c.1389G>A synonymous_variant 0.29
embB 4248606 p.Leu698Gln missense_variant 0.15
embB 4249218 p.Tyr902Cys missense_variant 0.11
aftB 4267429 p.Ser470Pro missense_variant 0.14
aftB 4268863 c.-27G>A upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408143 c.60G>T synonymous_variant 0.13
gid 4408156 p.Leu16Arg missense_variant 1.0