TB-Profiler result

Run: SRR6855952
Summary

Run ID: SRR6855952

Sample name:

Date: 04-04-2023 17:51:05

Number of reads: 441755

Percentage reads mapped: 98.63

Strain: lineage4.1.1.3

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
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.99
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 2288719 p.Met175Val missense_variant 0.11 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8018 c.717C>T synonymous_variant 0.15
gyrA 8116 p.Thr272Ile missense_variant 0.2
gyrA 8218 p.Ser306Cys missense_variant 0.11
gyrA 8489 c.1188A>G synonymous_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575979 p.Asp211Val missense_variant 0.11
rpoB 759858 c.54_55delGC frameshift_variant 0.12
rpoB 761229 p.Gly475Ser missense_variant 0.11
rpoB 763159 p.Leu1118Gln missense_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766507 c.3138C>T synonymous_variant 0.11
rpoC 766810 c.3441G>A synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781435 c.-125G>C upstream_gene_variant 1.0
rplC 801051 c.243G>A synonymous_variant 0.12
rplC 801099 c.291T>C synonymous_variant 0.11
fbiC 1303241 p.Tyr104Phe missense_variant 0.13
fbiC 1304671 p.Val581Phe missense_variant 0.11
fbiC 1304951 p.Asp674Val missense_variant 0.12
Rv1258c 1407166 c.174delC frameshift_variant 0.13
atpE 1461056 c.12T>A synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475013 n.1356G>C non_coding_transcript_exon_variant 0.18
rrl 1475354 n.1697A>G non_coding_transcript_exon_variant 0.14
rrl 1476173 n.2516A>G non_coding_transcript_exon_variant 0.13
rrl 1476678 n.3024delT non_coding_transcript_exon_variant 0.1
rrl 1476706 n.3049C>A non_coding_transcript_exon_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101976 p.Pro356Leu missense_variant 0.11
ndh 2102244 p.Arg267Trp missense_variant 0.12
katG 2154428 p.Asn562Asp missense_variant 0.1
katG 2155056 p.Gln352His missense_variant 0.11
katG 2156240 c.-130dupC upstream_gene_variant 0.15
PPE35 2168798 c.1815T>C synonymous_variant 0.13
PPE35 2169503 c.1109delG frameshift_variant 0.11
PPE35 2170312 p.Arg101Trp missense_variant 0.5
PPE35 2170652 c.-40C>G upstream_gene_variant 0.2
Rv1979c 2222013 c.1152C>A synonymous_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288690 c.552C>T synonymous_variant 0.13
pncA 2289464 c.-223A>T upstream_gene_variant 0.12
pncA 2290224 c.-983A>T upstream_gene_variant 0.22
kasA 2517975 c.-140A>C upstream_gene_variant 0.11
eis 2714398 p.His312Arg missense_variant 0.12
pepQ 2860475 c.-57C>A upstream_gene_variant 0.11
Rv2752c 3066245 c.-54C>T upstream_gene_variant 0.15
thyX 3067414 p.Ala178Pro missense_variant 0.12
thyA 3074371 p.Met34Thr missense_variant 0.11
thyA 3074637 c.-166A>G upstream_gene_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448939 p.Asp146His missense_variant 0.15
Rv3083 3449938 p.Asp479Asn missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4241060 p.Pro400Thr missense_variant 0.11
embC 4241848 c.1986C>A synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243421 c.189A>G synonymous_variant 0.11
embA 4243692 p.Gly154Arg missense_variant 0.25
embB 4248909 p.Ala799Val missense_variant 0.1
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4267605 p.Arg411Pro missense_variant 0.22
whiB6 4338326 p.Ala66Thr missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 1.0
gid 4407829 p.Gln125Arg missense_variant 0.11