TB-Profiler result

Run: SRR2101504
Summary

Run ID: SRR2101504

Sample name:

Date: 03-04-2023 23:45:28

Number of reads: 815608

Percentage reads mapped: 98.34

Strain: lineage4.3.4.1;lineage3.1.2

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
lineage3 East-African-Indian CAS RD750 0.37
lineage4 Euro-American LAM;T;S;X;H None 0.63
lineage4.3 Euro-American (LAM) mainly-LAM None 0.58
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.42
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.35
lineage4.3.4 Euro-American (LAM) LAM RD174 0.64
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 0.59
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
fgd1 491742 c.960T>C synonymous_variant 0.33
rpoB 759746 c.-61C>T upstream_gene_variant 0.23
rpoC 762434 c.-936T>G upstream_gene_variant 0.39
rpoC 763031 c.-339T>C upstream_gene_variant 0.45
rpoC 764995 c.1626C>G synonymous_variant 0.61
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.46
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.43
PPE35 2167926 p.Leu896Ser missense_variant 0.37
PPE35 2168604 p.Pro670Leu missense_variant 0.28
PPE35 2170231 p.Gln128Lys missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.41
pncA 2289365 c.-125delC upstream_gene_variant 0.24
ahpC 2726105 c.-88G>A upstream_gene_variant 0.27
pepQ 2859546 c.873T>G synonymous_variant 0.41
thyA 3073868 p.Thr202Ala missense_variant 0.63
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 0.7
fbiA 3640524 c.-19G>T upstream_gene_variant 0.11
alr 3841546 c.-126C>A upstream_gene_variant 0.59
alr 3841612 c.-193_-192insC upstream_gene_variant 0.6
clpC1 4038287 c.2418C>T synonymous_variant 0.65
embC 4242075 p.Arg738Gln missense_variant 0.34
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249691 p.Asp1060Tyr missense_variant 0.12
aftB 4268720 c.117C>A synonymous_variant 0.13
ethA 4326181 p.Phe431Leu missense_variant 0.27
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.23
gid 4408156 p.Leu16Arg missense_variant 0.71