TB-Profiler result

Run: SRR22196586
Summary

Run ID: SRR22196586

Sample name:

Date: 04-04-2023 04:06:14

Number of reads: 415497

Percentage reads mapped: 18.41

Strain: lineage4.1.2.1

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
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
pncA 2288971 p.Glu91* stop_gained 0.2 pyrazinamide
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 7263 p.Val675Ala missense_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9345 p.Arg682Gly missense_variant 0.29
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760060 p.Tyr85Cys missense_variant 0.17
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 763101 p.Ala1099Thr missense_variant 0.29
rpoB 763111 p.Lys1102Arg missense_variant 0.25
rpoC 764059 c.693delC frameshift_variant 0.2
rpoC 765110 p.Met581Val missense_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765506 p.Val713Ile missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775723 p.Ile920Val missense_variant 0.2
mmpL5 776926 p.Thr519Ala missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303364 p.Phe145Ser missense_variant 0.12
fbiC 1303438 p.Thr170Ser missense_variant 0.29
fbiC 1304632 p.Ala568Ser missense_variant 0.15
fbiC 1305176 p.Ser749* stop_gained 0.27
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.18
rrl 1475174 n.1517C>T non_coding_transcript_exon_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101921 c.1122G>T synonymous_variant 0.2
ndh 2103113 c.-71C>G upstream_gene_variant 0.15
ndh 2103134 c.-92T>A upstream_gene_variant 0.13
PPE35 2170571 p.Leu14Phe missense_variant 0.17
Rv1979c 2222243 p.Ala308Pro missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
folC 2746473 p.Val376Ile missense_variant 0.4
thyX 3067874 c.72C>A synonymous_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3613142 c.-26A>G upstream_gene_variant 0.25
embC 4240246 c.384C>T synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4246280 c.-234G>T upstream_gene_variant 1.0
embB 4248015 p.Thr501Arg missense_variant 0.15
aftB 4268279 c.558G>A synonymous_variant 0.29
aftB 4269252 c.-416C>T upstream_gene_variant 0.17
ethR 4327760 p.Val71Glu missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408129 p.Ala25Val missense_variant 0.13