TB-Profiler result

Run: SRR6982338
Summary

Run ID: SRR6982338

Sample name:

Date: 04-04-2023 18:34:33

Number of reads: 433053

Percentage reads mapped: 99.64

Strain: lineage4.3.4.1

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
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 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 7729 p.Arg143Lys missense_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9353 c.2052G>A synonymous_variant 0.11
fgd1 491019 p.Phe79Leu missense_variant 0.12
mshA 575160 c.-187delT upstream_gene_variant 0.13
mshA 575662 c.319delG frameshift_variant 0.11
mshA 575812 p.Tyr155* stop_gained 0.15
mshA 576491 p.Arg382Ser missense_variant 1.0
rpoB 762059 p.Ile751Met missense_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765738 p.Arg790Leu missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775995 p.Ile829Thr missense_variant 0.1
mmpL5 777874 p.Ser203Gly missense_variant 0.13
mmpR5 779289 p.Phe100Leu missense_variant 0.13
mmpR5 779363 p.Leu125Pro missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304654 p.Asp575Gly missense_variant 0.1
fbiC 1305037 p.Arg703Trp missense_variant 0.11
Rv1258c 1407210 p.Ala44Asp missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834946 p.Gln469Lys missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103030 c.12delG frameshift_variant 0.2
katG 2154405 c.1707G>T synonymous_variant 0.11
katG 2155179 c.933C>T synonymous_variant 0.2
Rv1979c 2222854 p.Ile104Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714689 p.Phe215Ser missense_variant 0.2
Rv2752c 3064662 p.Lys510Asn missense_variant 0.12
Rv2752c 3064747 p.Gly482Asp missense_variant 0.17
thyX 3067603 p.Arg115Trp missense_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086886 p.Val23Ile missense_variant 0.12
ald 3086993 c.174C>T synonymous_variant 0.1
fbiD 3339575 p.Ala153Glu missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474145 p.Gly47Trp missense_variant 0.12
fprA 3474774 c.768G>A synonymous_variant 0.12
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612251 p.Ser289* stop_gained 0.17
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039617 p.Arg363Gln missense_variant 0.18
clpC1 4039991 c.714G>A synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242787 c.-446G>A upstream_gene_variant 0.12
embA 4245319 c.2088delC frameshift_variant 0.12
ethA 4326777 p.Met233Val missense_variant 0.1
ethR 4327423 c.-126G>T upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0