TB-Profiler result

Run: ERR5866078
Summary

Run ID: ERR5866078

Sample name:

Date: 02-04-2023 00:29:41

Number of reads: 1425875

Percentage reads mapped: 98.9

Strain: lineage4.2.1.1

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
lineage4.2.1.1 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 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
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
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776802 p.Met560Thr missense_variant 1.0
mmpL5 777451 p.Val344Leu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.16
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.16
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.16
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.15
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.11
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.19
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.2
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.18
inhA 1673925 c.-277C>A upstream_gene_variant 0.11
inhA 1674212 p.Leu4Pro missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102983 c.60C>T synonymous_variant 0.11
PPE35 2169879 p.Phe245Cys missense_variant 1.0
Rv1979c 2221805 p.Ile454Phe missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065958 c.234G>A synonymous_variant 1.0
thyA 3074166 c.306G>A synonymous_variant 0.15
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
ddn 3987092 p.Glu83Asp missense_variant 1.0
clpC1 4039162 p.His515Asp missense_variant 0.11
clpC1 4040786 c.-82G>A upstream_gene_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 1.0