TB-Profiler result

Run: ERR501642
Summary

Run ID: ERR501642

Sample name:

Date: 01-04-2023 21:48:23

Number of reads: 444545

Percentage reads mapped: 99.27

Strain: lineage4.3.2.1

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 0.99
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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 5150 c.-90G>A upstream_gene_variant 0.12
gyrB 5520 p.Pro94Leu missense_variant 1.0
gyrA 7123 c.-179C>T upstream_gene_variant 0.15
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9482 c.2181G>T synonymous_variant 0.25
fgd1 490717 c.-66C>T upstream_gene_variant 0.18
rpoB 761622 p.Gln606Lys missense_variant 0.13
rpoB 762816 p.Leu1004Phe missense_variant 0.29
rpoC 762836 c.-534C>G upstream_gene_variant 0.22
rpoC 764120 p.Tyr251Asn missense_variant 0.13
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801361 p.Val185Phe missense_variant 0.29
embR 1417374 c.-27G>T upstream_gene_variant 0.5
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rpsA 1834395 p.Arg285Gln missense_variant 0.18
rpsA 1834555 c.1014T>A synonymous_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918311 p.Asn124Lys missense_variant 0.18
ndh 2102362 c.680delA frameshift_variant 0.2
katG 2156506 c.-395G>A upstream_gene_variant 0.13
PPE35 2170117 p.Pro166Ala missense_variant 0.2
Rv1979c 2222037 c.1128C>A synonymous_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290025 c.-784C>G upstream_gene_variant 0.17
eis 2715442 c.-110G>A upstream_gene_variant 0.15
ahpC 2726063 c.-130C>T upstream_gene_variant 0.29
ahpC 2726338 p.Val49Gly missense_variant 0.4
folC 2746176 p.Ala475Ser missense_variant 0.18
folC 2747170 c.429T>C synonymous_variant 0.25
pepQ 2860532 c.-114G>T upstream_gene_variant 0.2
ribD 2987240 c.402C>T synonymous_variant 0.2
Rv2752c 3065673 c.519C>T synonymous_variant 0.29
Rv2752c 3067017 c.-826G>A upstream_gene_variant 0.15
thyX 3067640 c.306G>T synonymous_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074455 p.Asp6Val missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338956 c.-162G>T upstream_gene_variant 0.18
fbiD 3339229 p.Val38Met missense_variant 0.17
fbiD 3339273 c.156T>G synonymous_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474013 p.Pro3Ser missense_variant 0.13
Rv3236c 3612865 c.252C>T synonymous_variant 0.2
Rv3236c 3612987 p.Gly44Ser missense_variant 0.33
rpoA 3877588 c.918_919delGT frameshift_variant 0.17
rpoA 3877727 p.Tyr261His missense_variant 0.29
ddn 3986928 p.Tyr29Asn missense_variant 0.14
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4239770 c.-93C>T upstream_gene_variant 0.22
embC 4240435 p.Tyr191* stop_gained 0.14
embC 4241155 c.1293C>T synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243420 p.Val63Glu missense_variant 0.2
embA 4245799 p.Trp856* stop_gained 0.22
embB 4247115 p.Ala201Val missense_variant 0.12
embB 4248291 p.Val593Glu missense_variant 0.25
ubiA 4269386 p.Ile150Phe missense_variant 0.29
ethA 4326419 p.Ala352Val missense_variant 0.5
ethA 4327041 p.Glu145Lys missense_variant 0.15
ethA 4328313 c.-840C>T upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0