TB-Profiler result

Run: SRR12830374
Summary

Run ID: SRR12830374

Sample name:

Date: 03-04-2023 06:58:28

Number of reads: 587804

Percentage reads mapped: 99.86

Strain: lineage4.3.4.2

Drug-resistance: Sensitive

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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
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 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
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
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765505 c.2136C>A synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776225 c.2255delA frameshift_variant 0.11
mmpR5 779269 c.282delG frameshift_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473050 n.1205A>T non_coding_transcript_exon_variant 0.13
rrl 1473676 n.19G>T non_coding_transcript_exon_variant 0.14
rrl 1474033 n.376A>G non_coding_transcript_exon_variant 0.15
rrl 1474043 n.386G>T non_coding_transcript_exon_variant 0.17
rrl 1474365 n.708G>T non_coding_transcript_exon_variant 0.18
rrl 1475828 n.2171G>T non_coding_transcript_exon_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155546 p.Asp189Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289451 c.-210G>T upstream_gene_variant 0.12
eis 2715442 c.-110G>T upstream_gene_variant 0.12
ahpC 2726410 p.Asp73Val missense_variant 0.12
Rv2752c 3065293 p.Val300Ala 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
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612334 p.Met261Ile missense_variant 0.14
Rv3236c 3612342 p.Ala259Ser missense_variant 0.14
rpoA 3877665 c.843C>T synonymous_variant 0.13
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4239763 c.-100C>T upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247884 c.1371C>A synonymous_variant 1.0
ethA 4326744 p.Leu244Met missense_variant 0.12
ethR 4327552 p.Thr2Pro missense_variant 1.0
ethR 4327555 p.Thr3Ala missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0