TB-Profiler result

Run: SRR4033508
Summary

Run ID: SRR4033508

Sample name:

Date: 04-04-2023 06:08:30

Number of reads: 869666

Percentage reads mapped: 99.74

Strain: lineage4.3.2.1

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
lineage4.3 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
pncA 2289057 p.Pro62Gln missense_variant 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 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
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775651 p.Arg944Trp missense_variant 0.14
mmpL5 776543 c.1937delA frameshift_variant 0.33
mmpS5 778608 p.Ala100Thr missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304759 p.Pro610Leu missense_variant 0.12
embR 1417341 p.Gly3Ser missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1473883 n.226A>G non_coding_transcript_exon_variant 0.22
rpsA 1834938 p.Ser466Asn missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2987307 p.Ala157Pro missense_variant 0.21
thyX 3067733 c.211_212delTC frameshift_variant 0.12
thyX 3068110 c.-165G>A upstream_gene_variant 0.22
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074114 p.Arg120Cys missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087167 c.348C>G synonymous_variant 0.22
ald 3087857 c.1038C>T synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568869 c.-190C>T upstream_gene_variant 0.17
alr 3841612 c.-193_-192insC upstream_gene_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040404 p.Asn101Tyr missense_variant 0.13
embC 4240584 p.Thr241Ile missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245341 c.2109C>A synonymous_variant 0.12
embB 4246585 c.72C>T synonymous_variant 0.29
aftB 4267949 c.888C>T synonymous_variant 0.13
ethA 4327479 c.-6G>A upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0