TB-Profiler result

Run: ERR2510793
Summary

Run ID: ERR2510793

Sample name:

Date: 31-03-2023 18:56:29

Number of reads: 1259481

Percentage reads mapped: 94.8

Strain: lineage4.3.3

Drug-resistance: MDR-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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
rpoB 761110 p.Asp435Val missense_variant 0.96 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.86 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.11 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289099 p.Lys48Thr missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326341 p.Pro378Leu missense_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576482 p.Val379Leu missense_variant 0.32
mshA 576516 p.Val390Ala missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_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 1472102 n.257G>A non_coding_transcript_exon_variant 0.13
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.18
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.12
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.14
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.25
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.18
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.14
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.13
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.13
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.19
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.16
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.18
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.18
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.17
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.17
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.16
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.15
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.24
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.17
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.17
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.17
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.19
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.13
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.11
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.12
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.12
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.21
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.22
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.24
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.23
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.15
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.24
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.38
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.23
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.28
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.24
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.22
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.2
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.2
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.19
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.19
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.19
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.18
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.18
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.22
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.22
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.13
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.13
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 0.11
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.14
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.17
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.17
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.15
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.21
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.17
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.17
PPE35 2170053 p.Thr187Ser missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243392 p.Asn54Asp missense_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.57
ubiA 4269731 p.Ala35Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407986 p.Gly73Arg missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0