TB-Profiler result

Run: SRR4035705
Summary

Run ID: SRR4035705

Sample name:

Date: 04-04-2023 07:14:49

Number of reads: 789876

Percentage reads mapped: 99.48

Strain: lineage4.1.2

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 1.0
lineage4.1.2 Euro-American T;H None 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
ethA 4327363 c.110delA frameshift_variant 0.12 ethionamide, ethionamide
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 5866 c.627C>A synonymous_variant 0.13
gyrB 6541 p.Asp434Glu missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7624 c.324delG frameshift_variant 0.15
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
ccsA 620168 p.Ala93Val missense_variant 0.18
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 762373 p.Pro856Leu missense_variant 0.13
rpoB 762732 c.2927delA frameshift_variant 0.2
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 767133 p.Gly1255Asp missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpS5 779683 c.-778G>T upstream_gene_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781662 c.106delC frameshift_variant 0.12
fbiC 1303016 p.Val29Gly missense_variant 0.2
fbiC 1304382 c.1452G>A synonymous_variant 0.12
atpE 1460872 c.-173G>T upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833359 c.-183T>C upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101937 p.Ser369Leu missense_variant 0.11
PPE35 2168733 p.Thr627Ile missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518185 p.Ser24* stop_gained 0.11
thyA 3073806 c.666C>G synonymous_variant 0.5
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612525 p.Ala198Ser missense_variant 0.15
fbiB 3641624 p.Ser30Arg missense_variant 0.25
fbiB 3642672 c.1140delC frameshift_variant 0.2
alr 3841496 c.-76A>G upstream_gene_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246744 c.231C>T synonymous_variant 0.14
ethA 4327428 p.Gly16Ser missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0