TB-Profiler result

Run: SRR1166872
Summary

Run ID: SRR1166872

Sample name:

Date: 03-04-2023 01:27:46

Number of reads: 1655405

Percentage reads mapped: 85.56

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 0.99
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_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 0.93
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764387 c.1018T>C synonymous_variant 0.11
rpoC 764942 p.His525Asn missense_variant 0.98
rpoC 764995 c.1626C>G synonymous_variant 0.95
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.97
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.11
rrs 1472574 n.729T>G non_coding_transcript_exon_variant 0.1
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.13
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.11
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.12
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.12
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.12
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.11
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.14
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.1
rrl 1476366 n.2709A>C non_coding_transcript_exon_variant 0.11
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.12
rrl 1476374 n.2717T>G non_coding_transcript_exon_variant 0.12
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.12
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.12
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.14
rrl 1476427 n.2770G>T non_coding_transcript_exon_variant 0.12
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.12
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
pepQ 2860148 p.Gly91Ser missense_variant 0.13
pepQ 2860162 c.256_257insCGGCCGGCCAGGTAGCGCCCGACC conservative_inframe_insertion 0.14
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.98
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 0.97
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407905 p.Phe100Val missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0