TB-Profiler result

Run: SRR4033494
Summary

Run ID: SRR4033494

Sample name:

Date: 04-04-2023 06:07:58

Number of reads: 694541

Percentage reads mapped: 99.69

Strain: lineage4.3.2.1

Drug-resistance: Sensitive

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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 1.0
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
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 7609 p.Trp103* stop_gained 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575956 c.610delC frameshift_variant 0.11
ccsA 619899 c.9G>A synonymous_variant 0.14
rpoB 761560 p.Thr585Ser missense_variant 0.15
rpoC 764148 p.Ser260Leu missense_variant 0.18
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776647 p.Val612Ile missense_variant 0.17
mmpL5 777559 p.His308Tyr missense_variant 0.22
mmpS5 778682 p.Asp75Gly missense_variant 0.4
mmpS5 778820 p.Arg29His missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304348 p.Trp473Leu missense_variant 0.15
Rv1258c 1406744 c.597G>A synonymous_variant 0.14
Rv1258c 1407485 c.-145G>A upstream_gene_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471866 n.21C>T non_coding_transcript_exon_variant 0.17
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1474931 n.1274G>A non_coding_transcript_exon_variant 0.4
rrl 1475354 n.1697A>T non_coding_transcript_exon_variant 0.5
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.33
rrl 1475957 n.2304delC non_coding_transcript_exon_variant 0.29
rpsA 1833729 c.191_192delCC frameshift_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153970 p.Asp714Glu missense_variant 0.12
katG 2155419 p.Asn231Lys missense_variant 0.25
katG 2155443 c.669G>A synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289318 c.-77G>C upstream_gene_variant 0.2
kasA 2518992 p.Arg293His missense_variant 0.12
eis 2715225 p.Trp36Cys missense_variant 0.11
folC 2746766 p.Gln278Arg missense_variant 0.15
folC 2747565 p.Gly12* stop_gained 0.33
ribD 2987446 p.Val203Ala missense_variant 0.2
Rv2752c 3064785 c.1407G>T synonymous_variant 0.2
Rv2752c 3067112 c.-921G>A upstream_gene_variant 0.13
thyX 3067662 p.Arg95Leu missense_variant 0.14
thyX 3068114 c.-169G>T upstream_gene_variant 0.4
thyA 3073805 p.Glu223* stop_gained 0.29
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640392 c.-151A>G upstream_gene_variant 0.13
fbiA 3640791 p.Asp83Glu missense_variant 0.18
fbiB 3641955 p.Gly141Arg missense_variant 0.18
alr 3840384 p.Phe346Ser missense_variant 0.25
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038497 c.2208C>T synonymous_variant 0.12
embC 4240509 p.Ala216Val missense_variant 0.12
embC 4241323 c.1464delT frameshift_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243036 c.-197C>A upstream_gene_variant 0.11
embA 4245924 p.Val898Ile missense_variant 0.25
embB 4248318 p.Val602Ala missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0