TB-Profiler result

Run: SRR4033516
Summary

Run ID: SRR4033516

Sample name:

Date: 04-04-2023 06:08:48

Number of reads: 1353114

Percentage reads mapped: 99.64

Strain: lineage4.3.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
gyrB 5516 p.Ile93Val missense_variant 0.14
gyrB 5520 p.Pro94Leu missense_variant 1.0
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 760228 p.Ile141Thr missense_variant 0.11
rpoC 763685 c.317delA frameshift_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778520 p.Thr129Asn missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781646 p.Gln29His missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.29
rrl 1476794 n.3137C>A splice_region_variant&non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918284 c.345C>T synonymous_variant 0.11
tlyA 1918526 c.591_593delGGT disruptive_inframe_deletion 0.12
PPE35 2167841 c.2772T>A synonymous_variant 0.15
PPE35 2169102 p.Pro504Leu missense_variant 0.12
PPE35 2170409 c.204G>A synonymous_variant 0.17
Rv1979c 2222675 p.Gly164* stop_gained 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2987553 p.Arg239Cys missense_variant 0.11
thyA 3073806 c.666C>G synonymous_variant 0.14
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475258 p.Val418Phe missense_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242303 p.Leu814Gln missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4327487 c.-15delT upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0