TB-Profiler result

Run: SRR16088231
Summary

Run ID: SRR16088231

Sample name:

Date: 03-04-2023 16:04:50

Number of reads: 2736117

Percentage reads mapped: 99.47

Strain: lineage4.2.1.1

Drug-resistance: Sensitive

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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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 None 1.0
lineage4.2.1.1 Euro-American (TUR) H3;H4 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
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 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9647 c.2346C>G synonymous_variant 0.14
mshA 576108 p.Ala254Gly missense_variant 0.14
mshA 576442 p.Cys365Trp missense_variant 0.19
mshA 576613 c.1266A>C synonymous_variant 0.25
mshA 576616 c.1269G>C synonymous_variant 0.42
rpoC 764367 p.Gly333Ala missense_variant 0.19
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777128 c.1353A>G synonymous_variant 0.13
mmpL5 777451 p.Val344Leu missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.19
mmpL5 779100 c.-620A>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1460876 c.-169G>A upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475225 n.1568A>G non_coding_transcript_exon_variant 0.4
rrl 1475977 n.2320A>C non_coding_transcript_exon_variant 0.67
inhA 1673401 c.-801G>A upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 0.97
PPE35 2169879 p.Phe245Cys missense_variant 1.0
PPE35 2170058 c.555G>A synonymous_variant 0.2
PPE35 2170065 p.Ala183Gly missense_variant 0.23
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.27
pepQ 2860159 p.Ala87Gly missense_variant 0.18
Rv2752c 3067157 c.-966G>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087818 p.Cys333Trp missense_variant 0.11
fbiD 3339734 p.Ala206Gly missense_variant 0.29
fbiD 3339751 p.Ala212Pro missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.4
rpoA 3878590 c.-83G>C upstream_gene_variant 0.25
rpoA 3878641 c.-134C>G upstream_gene_variant 0.77
embC 4240409 p.Pro183Ala missense_variant 0.3
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245835 p.Leu868Arg missense_variant 0.23
embB 4246527 p.Ala5Gly missense_variant 0.18
embB 4247016 p.Ser168Trp missense_variant 0.18
whiB6 4338200 p.Asp108His missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 1.0