TB-Profiler result

Run: ERR4383948
Summary

Run ID: ERR4383948

Sample name:

Date: 01-04-2023 05:43:25

Number of reads: 1074476

Percentage reads mapped: 99.5

Strain: lineage4.3

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
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
ethA 4327138 c.335delC frameshift_variant 0.5 ethionamide
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 5396 p.Ala53Thr missense_variant 0.25
gyrB 5575 c.336C>T synonymous_variant 0.2
gyrB 5663 p.Asp142Asn missense_variant 0.4
gyrB 5918 p.Ala227Thr missense_variant 0.4
gyrB 6398 p.Val387Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7736 c.435C>T synonymous_variant 0.29
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491571 p.Asp263Glu missense_variant 0.12
fgd1 491594 p.Ala271Val missense_variant 0.13
fgd1 491652 c.870C>G synonymous_variant 0.14
mshA 576108 p.Ala254Gly missense_variant 0.43
rpoB 759953 c.147C>T synonymous_variant 0.4
rpoB 760760 c.954C>A synonymous_variant 0.14
rpoC 762938 c.-432G>A upstream_gene_variant 0.13
rpoB 763152 p.Lys1116* stop_gained 0.2
rpoC 763157 c.-213G>T upstream_gene_variant 0.2
rpoB 763219 p.Ala1138Val missense_variant 0.33
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776224 p.Gly753Arg missense_variant 0.4
mmpL5 776460 p.Ala674Val missense_variant 0.22
mmpL5 776462 c.2017_2018delTC frameshift_variant 0.22
mmpL5 776516 p.Met655Ile missense_variant 0.67
mmpL5 778387 p.Ala32Pro missense_variant 0.15
mmpS5 778520 p.Thr129Asn missense_variant 0.18
mmpS5 778889 p.Lys6Met missense_variant 0.18
mmpS5 778927 c.-22C>T upstream_gene_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781519 c.-41A>T upstream_gene_variant 0.22
Rv1258c 1406491 p.Arg284Gly missense_variant 0.1
Rv1258c 1406600 c.741C>T synonymous_variant 0.13
embR 1416190 c.1158C>T synonymous_variant 1.0
embR 1417520 c.-173G>A upstream_gene_variant 0.15
embR 1417529 c.-182A>T upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473480 n.-178C>G upstream_gene_variant 0.67
rrl 1474570 n.913G>A non_coding_transcript_exon_variant 0.67
rrl 1475825 n.2168G>A non_coding_transcript_exon_variant 1.0
fabG1 1673270 c.-170G>A upstream_gene_variant 0.18
fabG1 1673323 c.-117C>T upstream_gene_variant 0.18
fabG1 1673593 p.Pro52Ser missense_variant 0.22
fabG1 1673820 p.Met127Ile missense_variant 0.15
inhA 1674198 c.-4G>A upstream_gene_variant 0.12
rpsA 1833995 p.Leu152Val missense_variant 0.22
rpsA 1834432 c.891G>C synonymous_variant 0.18
rpsA 1834639 c.1099delG frameshift_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918605 c.666C>T synonymous_variant 1.0
ndh 2102605 p.Glu146Asp missense_variant 0.12
ndh 2102730 c.312delC frameshift_variant 0.33
katG 2154279 c.1833C>T synonymous_variant 0.15
katG 2154397 p.Thr572Met missense_variant 0.14
katG 2154421 p.Thr564Met missense_variant 0.12
katG 2156013 c.99C>T synonymous_variant 0.12
katG 2156131 c.-22_-21delAC upstream_gene_variant 0.25
katG 2156337 c.-226G>A upstream_gene_variant 0.33
katG 2156433 c.-322C>G upstream_gene_variant 0.4
PPE35 2167662 p.Ser984Asn missense_variant 0.4
PPE35 2167739 c.2874C>T synonymous_variant 0.29
PPE35 2168623 p.Ala664Pro missense_variant 0.4
PPE35 2168627 c.1986C>T synonymous_variant 0.4
PPE35 2169142 c.1469_1470delTG frameshift_variant 0.2
PPE35 2170628 c.-16C>T upstream_gene_variant 0.17
Rv1979c 2221854 c.1311C>A synonymous_variant 0.5
Rv1979c 2222443 p.Ala241Val missense_variant 0.29
Rv1979c 2222835 c.330T>A synonymous_variant 0.29
Rv1979c 2223277 c.-113C>G upstream_gene_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289459 c.-218G>C upstream_gene_variant 0.1
ahpC 2726154 c.-39C>A upstream_gene_variant 0.15
ahpC 2726192 c.-1C>T upstream_gene_variant 0.29
ahpC 2726724 c.534delG frameshift_variant 0.33
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086891 c.72G>A synonymous_variant 0.18
ald 3087152 c.333C>T synonymous_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568634 p.Pro16Ala missense_variant 0.25
rpoA 3878308 p.Pro67Leu missense_variant 0.22
rpoA 3878365 p.Gly48Val missense_variant 0.2
ddn 3986875 p.Ser11Leu missense_variant 0.15
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039739 c.966C>T synonymous_variant 0.13
clpC1 4039969 p.Gln246Glu missense_variant 0.11
clpC1 4040830 c.-126G>A upstream_gene_variant 0.12
panD 4044111 c.171C>T synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248221 p.Pro570Ser missense_variant 0.12
embB 4248319 c.1806A>T synonymous_variant 0.25
ubiA 4269323 p.Pro171Thr missense_variant 0.13
ubiA 4269368 p.Ala156Pro missense_variant 0.12
ethR 4326622 c.-927C>T upstream_gene_variant 0.17
ethR 4327192 c.-357G>A upstream_gene_variant 0.25
ethA 4327227 p.Glu83Lys missense_variant 0.4
ethA 4327265 p.Thr70Ile missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338627 c.-106T>C upstream_gene_variant 0.5
gid 4408156 p.Leu16Arg missense_variant 1.0