TB-Profiler result

Run: ERR7801249

Summary

Run ID: ERR7801249

Sample name:

Date: 02-04-2023 06:00:16

Number of reads: 576250

Percentage reads mapped: 99.43

Strain: lineage4.3.4.2

Drug-resistance: Sensitive


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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 0.99
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
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 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7892 c.591G>T synonymous_variant 0.17
gyrA 9155 c.1854C>A synonymous_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9597 c.2296T>C synonymous_variant 0.13
fgd1 491589 p.Glu269Asp missense_variant 0.13
mshA 575321 c.-27G>A upstream_gene_variant 0.15
ccsA 620072 p.Pro61His missense_variant 0.33
ccsA 620371 p.Ala161Thr missense_variant 0.25
ccsA 620612 p.Gly241Val missense_variant 0.17
rpoB 762769 p.Pro988His missense_variant 0.14
rpoC 764541 p.Val391Gly missense_variant 0.14
rpoC 764544 p.Thr392Asn missense_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765332 p.Gly655Cys missense_variant 0.2
mmpL5 775616 c.2865G>A synonymous_variant 0.22
mmpL5 775620 p.Ser954* stop_gained 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776282 c.2199G>A synonymous_variant 0.12
mmpL5 777021 p.Pro487Leu missense_variant 0.17
mmpL5 777357 p.Arg375Leu missense_variant 0.25
mmpL5 777766 c.713_714delTC frameshift_variant 0.22
mmpR5 778436 c.-554G>T upstream_gene_variant 0.21
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801130 p.Asp108Asn missense_variant 0.2
rplC 801269 p.Cys154Tyr missense_variant 0.18
rplC 801320 p.Gly171Asp missense_variant 0.18
fbiC 1303904 p.Leu325Pro missense_variant 0.12
fbiC 1304751 c.1821C>A synonymous_variant 0.15
Rv1258c 1406532 p.Gly270Val missense_variant 0.15
Rv1258c 1406621 c.720G>A synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102472 p.Glu191* stop_gained 0.14
katG 2155583 p.Gly177Cys missense_variant 0.17
katG 2155663 p.Pro150Gln missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.18
PPE35 2170053 p.Thr187Ser missense_variant 0.15
Rv1979c 2222478 c.687G>A synonymous_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288704 p.Val180Ile missense_variant 0.2
pncA 2289249 c.-8G>T upstream_gene_variant 0.15
kasA 2519082 p.Ala323Val missense_variant 0.4
folC 2747420 p.Pro60Arg missense_variant 0.17
pepQ 2859356 p.Ala355Ser missense_variant 0.2
pepQ 2860595 c.-177C>A upstream_gene_variant 0.17
Rv2752c 3066134 p.Ala20Thr missense_variant 0.29
thyX 3067294 p.Gln218Lys missense_variant 0.17
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086976 p.Ala53Ser missense_variant 0.12
Rv3083 3449597 c.1096delC frameshift_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474114 c.108C>T synonymous_variant 0.38
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612528 p.Ala197Ser missense_variant 0.14
fbiB 3641013 c.-522C>G upstream_gene_variant 0.12
fbiA 3641453 p.Arg304Leu missense_variant 0.15
fbiB 3641481 c.-54G>A upstream_gene_variant 0.18
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039358 c.1347C>T synonymous_variant 0.33
clpC1 4039363 p.Ala448Ser missense_variant 0.33
clpC1 4039394 c.1311G>T synonymous_variant 0.25
embC 4240290 p.Pro143Leu missense_variant 0.14
embC 4241381 p.Gly507Trp missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243427 c.195G>T synonymous_variant 0.18
embA 4243889 c.657G>T synonymous_variant 0.14
embA 4245496 p.Gly755Val missense_variant 0.18
embA 4246044 p.Val938Leu missense_variant 0.12
embB 4246577 p.Ser22Thr missense_variant 0.18
embB 4247072 p.Gly187Trp missense_variant 0.15
embB 4248445 c.1932C>T synonymous_variant 0.17
embB 4248862 c.2349C>G synonymous_variant 0.33
aftB 4267560 p.Ala426Asp missense_variant 0.14
ethR 4327249 c.-300G>T upstream_gene_variant 0.17
ethA 4327544 c.-71G>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 4408156 p.Leu16Arg missense_variant 1.0
gid 4408424 c.-222C>T upstream_gene_variant 0.15