TB-Profiler result

Run: ERR4818578
Summary

Run ID: ERR4818578

Sample name:

Date: 01-04-2023 15:38:13

Number of reads: 529049

Percentage reads mapped: 99.66

Strain: lineage4.6.2.2

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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 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
tlyA 1918700 c.764delG frameshift_variant 0.11 capreomycin
gid 4407851 c.351delG frameshift_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
gyrB 5261 c.25delC frameshift_variant 0.11
gyrB 6533 p.Ala432Ser missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8371 p.Arg357Gln missense_variant 0.11
gyrA 8710 p.Ala470Val missense_variant 0.29
gyrA 8807 p.Asp502Glu missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.17
fgd1 491001 c.219G>C synonymous_variant 0.13
fgd1 491636 p.Ile285Asn missense_variant 0.17
mshA 576492 p.Arg382His missense_variant 0.13
ccsA 620089 p.Gln67Lys missense_variant 0.33
rpoB 759686 c.-121G>A upstream_gene_variant 0.14
rpoB 763003 p.Glu1066Gly missense_variant 0.2
rpoC 764361 p.Asp331Val missense_variant 0.25
rpoC 764516 p.Asp383Asn missense_variant 0.29
rpoC 764757 p.Leu463Pro missense_variant 0.12
rpoC 764994 p.Ala542Val missense_variant 0.1
rpoC 765760 p.Asn797Lys missense_variant 0.13
rpoC 765788 p.Ala807Thr missense_variant 0.11
rpoC 766785 p.Gln1139Pro missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775956 p.Ile842Thr missense_variant 0.13
mmpL5 776341 c.2139delG frameshift_variant 0.1
mmpL5 777488 p.Tyr331* stop_gained 0.18
mmpL5 777630 p.Arg284His missense_variant 0.12
mmpL5 777911 c.570C>T synonymous_variant 0.14
mmpL5 778154 p.Tyr109* stop_gained 0.18
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
mmpR5 779162 p.Thr58Met missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.2
fbiC 1303859 p.Gly310Glu missense_variant 0.12
fbiC 1304896 c.1966C>T synonymous_variant 0.13
embR 1417267 c.81G>C synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471855 n.10G>A non_coding_transcript_exon_variant 0.15
rrs 1472918 n.1073A>T non_coding_transcript_exon_variant 0.33
rpsA 1834546 p.Asp335Glu missense_variant 0.2
rpsA 1834855 c.1314C>A synonymous_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155833 c.279C>A synonymous_variant 0.12
PPE35 2170226 c.386delA frameshift_variant 0.14
PPE35 2170298 c.315A>G synonymous_variant 0.13
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288798 c.444C>A synonymous_variant 0.12
kasA 2518234 p.Glu40Asp missense_variant 0.18
kasA 2519166 p.Gly351Asp missense_variant 0.15
eis 2714482 c.848_850delGAC disruptive_inframe_deletion 0.15
eis 2714512 p.Pro274Leu missense_variant 0.2
eis 2715141 c.192C>T synonymous_variant 0.2
eis 2715421 c.-89G>A upstream_gene_variant 0.22
ahpC 2726338 p.Val49Gly missense_variant 0.23
ribD 2986988 c.150C>T synonymous_variant 0.11
ribD 2987031 p.Pro65Ser missense_variant 0.12
ribD 2987415 p.Glu193Lys missense_variant 0.25
Rv2752c 3065067 c.1125C>T synonymous_variant 0.13
Rv2752c 3065258 p.Met312Val missense_variant 1.0
Rv2752c 3066284 c.-93G>A upstream_gene_variant 0.18
thyX 3067474 p.Pro158Ala missense_variant 1.0
thyA 3073734 c.738C>T synonymous_variant 0.12
thyA 3074648 c.-177T>G upstream_gene_variant 0.2
fbiD 3339685 p.Asp190Asn missense_variant 0.25
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473942 c.-65C>A upstream_gene_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474313 p.Ala103Thr missense_variant 0.2
whiB7 3568830 c.-152_-151insGC upstream_gene_variant 0.5
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
Rv3236c 3612663 c.454C>T synonymous_variant 0.14
fbiB 3642361 p.Val276Ala missense_variant 0.17
fbiB 3642442 p.Pro303Leu missense_variant 0.22
alr 3840307 p.Gly372Cys missense_variant 0.11
alr 3840527 c.894A>G synonymous_variant 0.12
alr 3841595 c.-175T>C upstream_gene_variant 0.11
clpC1 4038714 c.1989_1990dupCT frameshift_variant 0.11
clpC1 4039066 p.Gly547Arg missense_variant 0.17
clpC1 4040286 p.Gln140Leu missense_variant 0.12
panD 4044244 p.Ala13Asp missense_variant 0.14
embC 4241220 p.Ile453Asn missense_variant 0.13
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242952 c.-281T>C upstream_gene_variant 0.29
embA 4244082 p.Ala284Thr missense_variant 0.2
embA 4245071 c.1839G>T synonymous_variant 0.22
embB 4245653 c.-861C>T upstream_gene_variant 0.2
embB 4246545 p.Thr11Asn missense_variant 0.14
embB 4247470 c.957T>C synonymous_variant 0.13
embB 4248333 p.Ala607Val missense_variant 0.22
embB 4248891 p.Val793Ala missense_variant 0.12
embB 4248930 p.Pro806Leu missense_variant 0.12
embB 4249323 p.Ala937Glu missense_variant 0.25
aftB 4267272 p.Lys522Arg missense_variant 1.0
aftB 4267671 p.Ala389Glu missense_variant 0.18
ubiA 4269266 p.Gly190Ser missense_variant 0.18
ethA 4326020 p.Ala485Val missense_variant 0.13
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethR 4327700 p.Ala51Gly missense_variant 0.11
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408142 p.Arg21Gly missense_variant 0.14