TB-Profiler result

Run: SRR21677869
Summary

Run ID: SRR21677869

Sample name:

Date: 04-04-2023 02:49:01

Number of reads: 587501

Percentage reads mapped: 99.63

Strain: lineage4.9

Drug-resistance: Other

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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
lineage4.9 Euro-American (H37Rv-like) T1 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
pncA 2289207 p.Asp12Gly missense_variant 0.12 pyrazinamide
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
fgd1 491173 c.391C>A synonymous_variant 0.12
fgd1 491520 c.738C>A synonymous_variant 0.11
rpoC 762902 c.-468C>T upstream_gene_variant 0.12
rpoC 763666 c.297G>A synonymous_variant 0.14
rpoC 765916 c.2549delT frameshift_variant 0.1
mmpL5 775588 c.2893T>C stop_lost&splice_region_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776682 p.Leu600Pro missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801265 p.Gly153Arg missense_variant 0.45
fbiC 1304051 p.Leu374Ser missense_variant 0.12
fbiC 1305026 p.Glu699Val missense_variant 0.11
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473738 n.81G>T non_coding_transcript_exon_variant 0.12
inhA 1674621 c.420C>T synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154591 c.1521C>T synonymous_variant 0.13
PPE35 2167657 p.Thr986Ala missense_variant 1.0
PPE35 2168293 c.2320T>C synonymous_variant 0.1
PPE35 2169482 c.1131G>A synonymous_variant 0.13
PPE35 2170147 p.Ser156Ala missense_variant 0.14
Rv1979c 2223263 c.-99T>C upstream_gene_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289940 c.-699C>T upstream_gene_variant 0.2
pncA 2290010 c.-769G>A upstream_gene_variant 0.12
pncA 2290061 c.-820C>G upstream_gene_variant 0.12
kasA 2518713 p.Gly200Ala missense_variant 0.12
eis 2715364 c.-32C>T upstream_gene_variant 0.1
folC 2746148 p.Arg484His missense_variant 0.11
Rv2752c 3064613 p.Ile527Phe missense_variant 0.1
thyX 3067987 c.-42C>A upstream_gene_variant 0.11
thyA 3074436 c.36C>T synonymous_variant 0.1
fbiB 3640755 c.-780C>T upstream_gene_variant 0.11
fbiA 3640836 c.297dupC frameshift_variant 0.14
fbiB 3641964 c.430_431insATT disruptive_inframe_insertion 0.12
fbiB 3642084 p.Gly184Arg missense_variant 0.13
rpoA 3877505 p.Ala335Thr missense_variant 0.1
rpoA 3877559 p.Pro317Thr missense_variant 0.11
clpC1 4038569 c.2136C>T synonymous_variant 1.0
panD 4044045 c.237G>A synonymous_variant 0.12
embC 4240556 c.696dupC frameshift_variant 0.11
embA 4243968 p.Val246Phe missense_variant 0.11
embA 4246079 p.Ser949Arg missense_variant 0.1
embB 4249489 c.2976G>A synonymous_variant 0.14
ubiA 4269311 p.Trp175Arg missense_variant 0.11
ethA 4327155 p.Ala107Ser missense_variant 0.1
ethA 4327445 p.Val10Ala missense_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338600 c.-79T>C upstream_gene_variant 1.0
fbiC 1305494 c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN frameshift_variant&stop_lost&splice_region_variant 1.0