TB-Profiler result

Run: ERR5865106
Summary

Run ID: ERR5865106

Sample name:

Date: 01-04-2023 23:48:08

Number of reads: 3594477

Percentage reads mapped: 94.74

Strain: lineage4.2.1

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
lineage4.2 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
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.12 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, 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 9304 p.Gly668Asp 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 1472172 n.327T>C non_coding_transcript_exon_variant 0.1
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.11
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.15
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.16
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.15
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.15
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.12
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.11
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.1
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.1
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.11
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.11
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.12
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.11
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.1
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.14
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.12
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.12
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.1
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.11
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.15
rrl 1475757 n.2100_2101insG non_coding_transcript_exon_variant 0.14
rrl 1475760 n.2105_2106delGC non_coding_transcript_exon_variant 0.13
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 0.13
rrl 1475765 n.2108A>T non_coding_transcript_exon_variant 0.13
rrl 1475769 n.2112_2113insC non_coding_transcript_exon_variant 0.16
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.16
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.16
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.15
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.14
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.15
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.14
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.1
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.11
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.12
rrl 1475963 n.2306G>A non_coding_transcript_exon_variant 0.12
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.11
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.11
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.12
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.11
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.12
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.13
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517966 c.-149G>A upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3877949 p.Thr187Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249594 c.3081G>A synonymous_variant 1.0
aftB 4268137 c.700C>T synonymous_variant 1.0
ethA 4328376 c.-903G>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408075 c.127delA frameshift_variant 1.0