TB-Profiler result

Run: SRR4037846
Summary

Run ID: SRR4037846

Sample name:

Date: 04-04-2023 07:42:58

Number of reads: 981853

Percentage reads mapped: 99.59

Strain: lineage4.3.2.1

Drug-resistance: RR-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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 0.99
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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 761106 p.Met434Leu missense_variant 0.15 rifampicin
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 5520 p.Pro94Leu missense_variant 1.0
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8507 c.1206C>T synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491221 p.Arg147Ser missense_variant 0.11
rpoB 759620 c.-187A>C upstream_gene_variant 0.23
rpoC 763860 c.493delC frameshift_variant 0.25
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765084 p.Arg572His missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777268 p.Leu405Met missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781454 c.-106G>A upstream_gene_variant 0.15
rpsL 781722 p.Val55Leu missense_variant 0.12
fbiC 1303534 p.Ser202Thr missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1472516 n.671C>G non_coding_transcript_exon_variant 0.11
rrl 1475140 n.1485delA non_coding_transcript_exon_variant 0.11
rpsA 1834142 p.Glu201Gln missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102859 c.183delG frameshift_variant 0.12
katG 2153964 c.2148G>A synonymous_variant 0.14
katG 2156558 c.-447G>A upstream_gene_variant 0.12
PPE35 2168035 p.Thr860Ala missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289127 p.Ala39Thr missense_variant 0.2
ahpC 2726732 p.Lys180Asn missense_variant 0.11
pepQ 2859593 p.Ala276Thr missense_variant 0.11
Rv2752c 3065663 p.Pro177Ser missense_variant 0.13
thyX 3067261 p.Asp229Asn missense_variant 0.17
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449308 p.Leu269Met missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640976 p.Ala145Val missense_variant 0.13
fbiB 3641955 p.Gly141Arg missense_variant 0.15
alr 3841213 p.Tyr70His missense_variant 0.17
rpoA 3878187 c.321C>T synonymous_variant 0.11
ddn 3986860 p.Pro6Gln missense_variant 0.11
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040225 c.479delG frameshift_variant 0.22
embC 4240556 p.Ala232Thr missense_variant 0.14
embC 4241314 c.1452G>C synonymous_variant 0.18
embC 4241436 p.Ala525Asp missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 0.93
embA 4244455 p.Ala408Val missense_variant 0.12
embA 4245472 p.Ala747Val missense_variant 0.11
embB 4246319 c.-195G>A upstream_gene_variant 0.17
embB 4247227 c.714C>A synonymous_variant 0.12
embB 4249382 p.Pro957Thr missense_variant 0.11
embB 4249396 p.Ile961Met missense_variant 0.13
ethA 4326504 p.Gly324* stop_gained 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0