TB-Profiler result

Run: ERR9119683
Summary

Run ID: ERR9119683

Sample name:

Date: 02-04-2023 10:01:31

Number of reads: 3083203

Percentage reads mapped: 49.78

Strain: lineage4.2.1

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
lineage4.2 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
gid 4408087 c.115delC 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
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 9647 c.2346C>G synonymous_variant 0.17
fgd1 491247 c.465C>T synonymous_variant 1.0
mshA 576442 p.Cys365Trp missense_variant 0.2
mshA 576616 c.1269G>C synonymous_variant 0.14
rpoC 764367 p.Gly333Ala missense_variant 0.3
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.12
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.11
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.11
rrs 1472677 n.832C>G non_coding_transcript_exon_variant 0.12
rrs 1472678 n.833T>A non_coding_transcript_exon_variant 0.12
rrs 1472697 n.852T>A non_coding_transcript_exon_variant 0.12
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.12
rrs 1472705 n.860G>A non_coding_transcript_exon_variant 0.11
rrs 1472708 n.863T>G non_coding_transcript_exon_variant 0.12
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.13
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.14
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.15
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.14
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.16
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.12
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.1
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.13
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.1
rrs 1473123 n.1278A>G non_coding_transcript_exon_variant 0.11
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.1
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.1
rrs 1473262 n.1417T>C non_coding_transcript_exon_variant 0.11
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.11
fabG1 1673553 p.Asp38Glu missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.39
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.21
pepQ 2860159 p.Ala87Gly missense_variant 0.23
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087816 p.Cys333Gly missense_variant 0.15
fbiD 3339734 p.Ala206Gly missense_variant 0.56
fbiD 3339751 p.Ala212Pro missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.29
rpoA 3878597 c.-90G>C upstream_gene_variant 0.18
rpoA 3878613 c.-106A>C upstream_gene_variant 0.33
rpoA 3878641 c.-134C>G upstream_gene_variant 0.56
embC 4240409 p.Pro183Ala missense_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.38
embB 4246529 p.Ser6Arg missense_variant 0.2
embB 4246584 p.Arg24Pro missense_variant 0.13
embB 4247028 p.Leu172Arg missense_variant 0.2
embB 4248328 c.1815G>C synonymous_variant 0.18
embB 4249594 c.3081G>A synonymous_variant 1.0
ethA 4328376 c.-903G>C upstream_gene_variant 1.0
ethA 4328415 c.-942A>G upstream_gene_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0