TB-Profiler result

Run: ERR4813296
Summary

Run ID: ERR4813296

Sample name:

Date: 01-04-2023 12:39:39

Number of reads: 324444

Percentage reads mapped: 99.3

Strain: lineage4.3.3

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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 761110 p.Asp435Val missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289213 p.Gln10Arg missense_variant 1.0 pyrazinamide
embB 4247469 p.Tyr319Ser missense_variant 1.0 ethambutol
gid 4407952 p.Pro84Leu missense_variant 1.0 streptomycin
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 6655 c.-647T>C upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7473 p.Ala58Thr missense_variant 0.13
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575642 p.Pro99Ser missense_variant 0.22
rpoB 760088 c.282C>T synonymous_variant 0.11
rpoB 761302 p.Arg499Leu missense_variant 0.17
rpoB 763102 p.Ala1099Glu missense_variant 0.11
rpoB 763126 p.Pro1107Gln missense_variant 0.11
rpoC 763142 c.-228C>T upstream_gene_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766757 p.Val1130Met missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775749 p.Gly911Asp missense_variant 0.15
mmpL5 777617 c.864A>G synonymous_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800671 c.-138G>A upstream_gene_variant 0.13
fbiC 1302889 c.-42G>A upstream_gene_variant 0.13
fbiC 1305246 p.Leu772Phe missense_variant 0.2
Rv1258c 1406783 c.558C>A synonymous_variant 0.14
embR 1417422 c.-75C>T upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834985 c.1445dupG frameshift_variant&stop_lost&splice_region_variant 1.0
tlyA 1917821 c.-119C>A upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102378 p.Pro222Arg missense_variant 0.22
ndh 2102485 c.558C>T synonymous_variant 0.14
katG 2154310 p.Gly601Val missense_variant 0.18
katG 2154316 p.Gly599Val missense_variant 0.18
katG 2154781 p.Ala444Val missense_variant 0.22
PPE35 2168601 p.Gly671Val missense_variant 0.2
PPE35 2168998 p.Ile539Val missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
eis 2714967 p.Glu122Asp missense_variant 0.29
ahpC 2726069 c.-124A>C upstream_gene_variant 0.2
pepQ 2860192 p.Glu76Gly missense_variant 1.0
Rv2752c 3066074 c.118C>T synonymous_variant 0.22
thyX 3067823 c.123G>T synonymous_variant 0.22
thyX 3067948 c.-3G>T upstream_gene_variant 0.33
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3073914 p.His186Gln missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338994 c.-124G>A upstream_gene_variant 0.5
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474921 c.915G>A synonymous_variant 1.0
Rv3236c 3612771 p.Val116Phe missense_variant 0.29
rpoA 3878308 p.Pro67Leu missense_variant 0.29
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4241284 c.1422G>T synonymous_variant 0.15
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243588 p.Arg119His missense_variant 0.33
embA 4244666 c.1434G>A synonymous_variant 0.67
embA 4244975 c.1743C>T synonymous_variant 0.33
embB 4248855 p.Gly781Asp missense_variant 0.18
aftB 4267165 p.Trp558Arg missense_variant 0.15
aftB 4268352 p.Leu162Arg missense_variant 0.4
aftB 4268515 p.Pro108Ser missense_variant 0.2
aftB 4268677 c.160C>A synonymous_variant 0.33
ubiA 4269151 p.Ala228Glu missense_variant 0.15
ethA 4327074 p.Leu134Phe missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0