TB-Profiler result

Run: SRR4035534
Summary

Run ID: SRR4035534

Sample name:

Date: 04-04-2023 07:09:31

Number of reads: 476191

Percentage reads mapped: 99.49

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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 761109 p.Asp435Tyr missense_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8056 p.Arg252Leu missense_variant 1.0
gyrA 9208 p.Lys636Met missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491498 p.Pro239Gln missense_variant 0.29
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776505 c.1975delC frameshift_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305186 c.2256C>T synonymous_variant 0.13
Rv1258c 1406790 p.Ser184Tyr missense_variant 0.2
embR 1417297 c.51A>G synonymous_variant 0.22
rrs 1471648 n.-197delC upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471673 n.-173C>T upstream_gene_variant 0.14
rrs 1471746 n.-100G>T upstream_gene_variant 0.18
rrs 1472401 n.559delG non_coding_transcript_exon_variant 0.29
rrl 1473609 n.-49G>A upstream_gene_variant 0.14
rrl 1474041 n.384T>G non_coding_transcript_exon_variant 0.2
rrl 1475029 n.1372T>G non_coding_transcript_exon_variant 0.67
rpsA 1833773 p.Glu78Lys missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101802 p.Leu414Gln missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
eis 2715258 c.75C>G synonymous_variant 0.18
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ribD 2987559 p.Ala241Ser missense_variant 0.5
thyX 3067599 p.Val116Gly missense_variant 0.4
thyA 3074424 c.48G>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4039948 p.Gly253* stop_gained 0.33
clpC1 4040611 p.His32Tyr missense_variant 0.29
embC 4240475 p.Ala205Thr missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245249 p.His673Tyr missense_variant 0.18
embA 4245977 p.Asp915Glu missense_variant 0.22
embB 4246994 p.Phe161Leu missense_variant 0.13
embB 4248160 c.1647C>T synonymous_variant 0.14
ubiA 4269128 p.Trp236Arg missense_variant 0.22
ethA 4326917 p.Thr186Met missense_variant 0.2
ethR 4327919 p.Gly124Asp missense_variant 0.12
ethA 4328212 c.-740delC upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0