TB-Profiler result

Run: SRR4033505
Summary

Run ID: SRR4033505

Sample name:

Date: 04-04-2023 06:08:20

Number of reads: 952849

Percentage reads mapped: 99.7

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 0.99
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 2288992 c.249delC frameshift_variant 0.12 pyrazinamide, 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
rpoB 759732 c.-75C>A upstream_gene_variant 0.2
rpoB 760120 p.Arg105Leu missense_variant 0.11
rpoB 762729 p.Gln975Lys missense_variant 0.13
rpoC 764426 p.Arg353Trp missense_variant 0.15
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776526 p.Met652Thr missense_variant 0.18
mmpL5 777484 c.996delT frameshift_variant 0.1
mmpL5 777661 p.Ala274Thr missense_variant 0.15
mmpR5 778996 c.8delT frameshift_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304826 c.1896G>T synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169689 c.924C>A synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223360 c.-196G>C upstream_gene_variant 0.18
Rv2752c 3065379 c.813C>T synonymous_variant 0.12
thyA 3073806 c.666C>G synonymous_variant 0.25
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
whiB7 3568848 c.-169G>T upstream_gene_variant 0.18
fbiB 3641955 p.Gly141Arg missense_variant 0.21
fbiB 3642455 c.921G>A synonymous_variant 0.11
alr 3840835 p.His196Asn missense_variant 0.12
ddn 3986739 c.-105T>C upstream_gene_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4241184 p.Thr441Met missense_variant 0.11
embC 4242425 p.Arg855Gly missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243486 p.Asn85Ser missense_variant 0.17
ethR 4327932 p.Arg128Ser missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0