TB-Profiler result

Run: SRR20139566
Summary

Run ID: SRR20139566

Sample name:

Date: 13-03-2023 09:16:10

Number of reads: 1008153

Percentage reads mapped: 99.59

Strain: lineage4.1.2.1

Drug-resistance: RR-TB

Download CSV Download TXT Download PDF Download JSON
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
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 761110 p.Asp435Val missense_variant 1.0 rifampicin
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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 5740 c.501G>C synonymous_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9301 p.Gly668Asp missense_variant 1.0
fgd1 490771 c.-12T>G upstream_gene_variant 0.16
fgd1 490780 c.-3C>A upstream_gene_variant 0.17
fgd1 490810 p.Ala10Thr missense_variant 0.16
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576705 p.Gln453Arg missense_variant 0.18
mshA 576710 p.Arg455Gly missense_variant 0.19
mshA 576732 p.Asp462Ala missense_variant 0.14
mshA 576735 p.Leu463Arg missense_variant 0.14
mshA 576741 p.Ala465Gly missense_variant 0.19
ccsA 620748 c.858T>G synonymous_variant 0.25
rpoB 759620 c.-187A>C upstream_gene_variant 0.15
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.13
fbiC 1303032 c.102A>G synonymous_variant 0.14
fbiC 1304146 p.Ile406Val missense_variant 0.18
fbiC 1304159 p.Val410Gly missense_variant 0.35
fbiC 1304166 c.1236A>G synonymous_variant 0.28
Rv1258c 1407039 p.Val101Gly missense_variant 0.16
Rv1258c 1407055 p.Tyr96Asp missense_variant 0.22
Rv1258c 1407061 p.Trp94Gly missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918004 p.Gln22Arg missense_variant 0.17
tlyA 1918010 p.Ala24Gly missense_variant 0.18
tlyA 1918066 p.Ala43Pro missense_variant 0.15
ndh 2102502 p.Thr181Pro missense_variant 0.14
ndh 2103235 c.-193C>G upstream_gene_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714548 p.Met262Leu missense_variant 0.2
eis 2714559 c.774C>G synonymous_variant 0.21
eis 2714566 p.Leu256Pro missense_variant 0.17
eis 2715468 c.-136C>T upstream_gene_variant 1.0
ahpC 2726350 p.Trp53Leu missense_variant 0.24
ahpC 2726394 p.Phe68Val missense_variant 0.15
thyA 3074645 c.-174T>G upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-10_-9insA upstream_gene_variant 1.0
fbiB 3642107 p.Glu191Asp missense_variant 0.12
clpC1 4039484 c.1221T>G synonymous_variant 0.15
embC 4240188 p.Val109Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
ethA 4326060 p.Lys472* stop_gained 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407983 c.217delG frameshift_variant 1.0