TB-Profiler result

Run: ERR190340
Summary

Run ID: ERR190340

Sample name:

Date: 31-03-2023 15:29:33

Number of reads: 780693

Percentage reads mapped: 99.41

Strain: lineage4.9;lineage3.1

Drug-resistance: HR-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
lineage3 East-African-Indian CAS RD750 0.6
lineage4 Euro-American LAM;T;S;X;H None 0.42
lineage4.9 Euro-American (H37Rv-like) T1 None 0.42
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.73
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
rrs 1473247 n.1402C>T non_coding_transcript_exon_variant 0.14 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.46 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 0.66
gyrA 8061 p.Arg254Ser missense_variant 0.14
gyrA 8978 c.1677C>T synonymous_variant 0.65
gyrA 9304 p.Gly668Asp missense_variant 0.68
fgd1 490751 c.-32T>G upstream_gene_variant 0.36
fgd1 491742 c.960T>C synonymous_variant 0.62
rpoB 759746 c.-61C>T upstream_gene_variant 0.52
rpoC 762434 c.-936T>G upstream_gene_variant 0.59
rpoC 763031 c.-339T>C upstream_gene_variant 0.65
rpoC 764410 c.1041G>A synonymous_variant 0.12
rpoC 764535 p.Arg389Pro missense_variant 0.19
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.44
mmpL5 777228 p.Arg418His missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673917 c.-285G>T upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101913 p.Ser377Trp missense_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 0.74
PPE35 2167926 p.Leu896Ser missense_variant 0.59
PPE35 2169866 c.747G>C synonymous_variant 0.21
PPE35 2170461 p.Gly51Glu missense_variant 0.71
Rv1979c 2223145 p.Arg7Lys missense_variant 0.32
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.77
pncA 2289365 c.-125delC upstream_gene_variant 0.54
pncA 2289448 c.-207G>A upstream_gene_variant 0.42
kasA 2518389 p.Gly92Glu missense_variant 0.11
ahpC 2726105 c.-88G>A upstream_gene_variant 0.44
folC 2747263 c.336C>A synonymous_variant 0.11
folC 2747754 c.-156C>T upstream_gene_variant 0.2
ribD 2987307 p.Ala157Pro missense_variant 0.29
Rv2752c 3067191 c.-1000G>A upstream_gene_variant 0.44
thyA 3073806 c.666C>G synonymous_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 0.56
fbiD 3339153 p.Leu12Phe missense_variant 0.2
fbiD 3339385 p.Asp90Asn missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.92
rpoA 3878641 c.-135delG upstream_gene_variant 0.17
clpC1 4038857 c.1848C>A synonymous_variant 0.18
embC 4240172 p.Val104Met missense_variant 0.71
embC 4241562 p.Arg567His missense_variant 0.65
embC 4242075 p.Arg738Gln missense_variant 0.64
embC 4242425 p.Arg855Gly missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 0.67
embA 4243323 p.Val31Ile missense_variant 0.5
ethA 4326969 p.Glu169Gln missense_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.75