TB-Profiler result

Run: ERR8773690
Summary

Run ID: ERR8773690

Sample name:

Date: 02-04-2023 08:14:26

Number of reads: 3469255

Percentage reads mapped: 90.32

Strain: lineage4.2.1

Drug-resistance: HR-TB

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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 0.99
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.98
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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.99 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 9808 p.Thr836Arg missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.1
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.2
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.2
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.2
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.2
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.17
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.15
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.23
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.23
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.23
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.2
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.31
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.29
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.29
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.29
rrs 1473001 n.1156G>C non_coding_transcript_exon_variant 0.22
rrs 1473002 n.1157G>A non_coding_transcript_exon_variant 0.22
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.23
rrs 1473008 n.1163C>T non_coding_transcript_exon_variant 0.23
rrs 1473009 n.1164T>G non_coding_transcript_exon_variant 0.23
rrs 1473020 n.1175T>C non_coding_transcript_exon_variant 0.23
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.14
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.14
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.15
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.26
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.29
rrl 1476353 n.2696G>A non_coding_transcript_exon_variant 0.32
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.3
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.3
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.32
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.33
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.34
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.33
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.3
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.31
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.21
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.19
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.2
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.2
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918591 p.Leu218Met missense_variant 1.0
tlyA 1918623 p.Ser228Arg missense_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747470 p.Ile43Ala missense_variant 0.98
ald 3086742 c.-78A>C upstream_gene_variant 0.98
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878599 c.-92C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247732 p.Ile407Ala missense_variant 0.98
embB 4249594 c.3081G>A synonymous_variant 0.99
ethA 4328376 c.-903G>C upstream_gene_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0