TB-Profiler result

Run: SRR8003011
Summary

Run ID: SRR8003011

Sample name:

Date: 13-08-2022 03:31:53

Number of reads: 2432099

Percentage reads mapped: 97.37

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289066 p.Ser59Phe missense_variant 0.99 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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
gyrB 5332 c.93C>T synonymous_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8168 p.Glu289Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.17
rpoC 766719 p.Asp1117Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472459 n.614C>T non_coding_transcript_exon_variant 0.18
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.27
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.23
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.23
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.38
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.15
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.25
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.14
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.21
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.21
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.14
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.15
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.38
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.38
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.38
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.38
rrl 1475953 n.2296A>G non_coding_transcript_exon_variant 0.23
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.42
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.42
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.5
rrl 1475978 n.2321C>T non_coding_transcript_exon_variant 0.4
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.36
rrl 1476363 n.2706A>G non_coding_transcript_exon_variant 0.2
rrl 1476366 n.2709A>C non_coding_transcript_exon_variant 0.2
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.2
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.3
rrl 1476374 n.2717T>G non_coding_transcript_exon_variant 0.2
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.3
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2170415 c.198A>G synonymous_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747470 p.Ile43Ala missense_variant 0.98
clpC1 4039729 p.Asp326Asn missense_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245417 p.Gly729Arg missense_variant 1.0
ethA 4327037 p.Gly146Asp missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0