TB-Profiler result

Run: SRR18715377
Summary

Run ID: SRR18715377

Sample name:

Date: 03-04-2023 20:31:38

Number of reads: 3672362

Percentage reads mapped: 99.67

Strain: lineage4.8;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 0.1
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.86
lineage4.1.2 Euro-American T;H None 0.11
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.14
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
gid 4407967 p.Leu79Ser missense_variant 0.88 streptomycin
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 0.15
gyrA 9304 p.Gly668Asp missense_variant 0.15
fgd1 490829 p.Ala16Val missense_variant 0.85
mshA 575679 p.Asn111Ser missense_variant 0.14
mshA 576108 p.Ala254Gly missense_variant 0.18
mshA 576113 p.Arg256Gly missense_variant 0.31
mshA 576456 p.Val370Gly missense_variant 0.27
mshA 576613 c.1266A>C synonymous_variant 0.41
mshA 576616 c.1269G>C synonymous_variant 0.21
rpoB 760115 c.309C>T synonymous_variant 0.13
rpoC 765150 p.Gly594Glu missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.82
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 0.94
PPE35 2170065 p.Ala183Gly missense_variant 0.3
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.12
ald 3087818 p.Cys333Trp missense_variant 0.12
fbiD 3339734 p.Ala206Gly missense_variant 0.4
fbiD 3339746 p.Ala210Val missense_variant 0.38
fbiD 3339749 p.Val211Gly missense_variant 0.17
fbiD 3339751 p.Ala212Pro missense_variant 0.23
rpoA 3878641 c.-134C>G upstream_gene_variant 0.75
embC 4240409 p.Pro183Ala missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.14
embB 4246527 p.Ala5Gly missense_variant 0.2
embB 4246584 p.Arg24Pro missense_variant 0.13
aftB 4269546 c.-710G>C upstream_gene_variant 0.9
ubiA 4269864 c.-31C>T upstream_gene_variant 0.83
whiB6 4338595 c.-75delG upstream_gene_variant 1.0