TB-Profiler result

Run: ERR9119081

Summary

Run ID: ERR9119081

Sample name:

Date: 02-04-2023 09:34:55

Number of reads: 470024

Percentage reads mapped: 99.58

Strain: lineage4.2.1

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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 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
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 7342 p.Arg14Leu missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7661 c.360C>T synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9485 c.2189delG frameshift_variant 0.12
mshA 576302 p.Leu319Met missense_variant 0.11
mshA 576535 c.1188T>C synonymous_variant 0.25
rpoB 760455 p.Gly217Cys missense_variant 0.14
rpoB 762099 p.Arg765Ser missense_variant 0.12
rpoB 762214 p.Lys803Arg missense_variant 0.12
rpoC 764532 p.Gly388Val missense_variant 0.12
rpoC 766256 p.Arg963Ser missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776470 p.Glu671* stop_gained 0.13
mmpL5 779070 c.-590G>A upstream_gene_variant 0.18
mmpR5 779378 p.Pro130Gln missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801356 p.His183Arg missense_variant 0.14
rplC 801459 p.Lys217Asn missense_variant 0.17
fbiC 1303789 p.Ile287Phe missense_variant 0.12
Rv1258c 1406866 p.Ala159Thr missense_variant 0.12
embR 1416549 c.798delC frameshift_variant 0.14
atpE 1460938 c.-107C>T upstream_gene_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155264 p.Leu283Arg missense_variant 0.22
PPE35 2169490 p.Gly375Trp missense_variant 0.22
PPE35 2169818 p.Asn265Lys missense_variant 0.25
PPE35 2169879 p.Phe245Cys missense_variant 1.0
PPE35 2170233 p.Gly127Val missense_variant 0.2
Rv1979c 2221862 p.Arg435Cys missense_variant 0.12
Rv1979c 2222004 c.1161C>T synonymous_variant 0.13
Rv1979c 2222025 c.1140C>A synonymous_variant 0.14
Rv1979c 2222664 c.501G>T synonymous_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518039 c.-76C>T upstream_gene_variant 0.12
kasA 2518469 p.Ala119Ser missense_variant 0.14
kasA 2518586 p.Leu158Phe missense_variant 0.11
eis 2714361 c.972C>A synonymous_variant 0.14
thyX 3067790 c.156C>A synonymous_variant 0.15
thyA 3074304 c.168C>T synonymous_variant 0.15
thyA 3074324 p.Val50Phe missense_variant 0.15
thyA 3074579 c.-108G>C upstream_gene_variant 0.15
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086800 c.-20C>T upstream_gene_variant 0.14
ald 3087925 p.Val369Glu missense_variant 0.12
fbiD 3339585 c.468C>A synonymous_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3613229 c.-113G>T upstream_gene_variant 0.11
fbiA 3640840 p.Asp100Asn missense_variant 0.12
fbiB 3642105 p.Glu191* stop_gained 0.18
alr 3841606 c.-186G>T upstream_gene_variant 0.12
rpoA 3878036 p.Glu158* stop_gained 0.22
panD 4043900 p.Ala128Thr missense_variant 0.12
embC 4239785 c.-78C>T upstream_gene_variant 0.12
embC 4240381 p.Gln173His missense_variant 0.11
embC 4240449 p.Gln196Leu missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245026 p.His598Gln missense_variant 0.18
embB 4246310 c.-204C>T upstream_gene_variant 1.0
embB 4247124 p.Ala204Val missense_variant 0.11
embB 4248686 p.Gly725Trp missense_variant 0.18
embB 4248744 p.Val744Asp missense_variant 0.1
embB 4248975 p.Leu821Pro missense_variant 0.14
embB 4249594 c.3081G>A synonymous_variant 1.0
aftB 4267847 c.990C>T synonymous_variant 0.4
aftB 4267855 c.982C>A synonymous_variant 0.4
ubiA 4269907 c.-74T>G upstream_gene_variant 0.12
ethA 4326421 c.1053G>C synonymous_variant 0.12
ethA 4326996 p.Pro160Ser missense_variant 0.18
ethA 4327409 p.His22Arg missense_variant 0.18
ethR 4327766 p.Leu73Pro missense_variant 0.12
ethA 4328376 c.-903G>C upstream_gene_variant 1.0
whiB6 4338268 p.Gly85Asp missense_variant 0.18
whiB6 4338461 p.Met21Leu missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407757 p.Ser149Ile missense_variant 0.11