TB-Profiler result

Run: SRR4035750
Summary

Run ID: SRR4035750

Sample name:

Date: 04-04-2023 07:16:28

Number of reads: 1485246

Percentage reads mapped: 99.56

Strain: lineage4.1.2

Drug-resistance: HR-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
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
katG 2154382 c.1729delG frameshift_variant 0.14 isoniazid
katG 2154961 p.Leu384Arg missense_variant 0.13 isoniazid
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 5514 p.Gly92Asp missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760240 p.Thr145Arg missense_variant 0.11
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776685 p.Ser599Leu missense_variant 0.15
mmpL5 777320 c.1161C>G synonymous_variant 0.95
mmpL5 777585 p.Tyr299Cys missense_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474950 n.1293G>A non_coding_transcript_exon_variant 0.12
rpsA 1834569 p.Asp343Gly missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167883 c.2730C>T synonymous_variant 0.18
PPE35 2170476 p.Gly46Ala missense_variant 0.1
Rv1979c 2223028 p.Phe46Tyr missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223349 c.-185G>T upstream_gene_variant 0.22
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
thyX 3067581 p.Met122Lys missense_variant 0.12
thyX 3067605 p.Ser114Trp missense_variant 0.1
thyX 3067658 c.288C>T synonymous_variant 0.13
thyA 3073806 c.666C>G synonymous_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 0.97
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
ubiA 4268960 p.Ile292Val missense_variant 0.12
ethA 4326341 p.Pro378His missense_variant 0.14
ethA 4326840 p.Ile212Val missense_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0