TB-Profiler result

Run: ERR4407535
Summary

Run ID: ERR4407535

Sample name:

Date: 01-04-2023 05:48:57

Number of reads: 273285

Percentage reads mapped: 99.57

Strain: lineage4.3

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 0.7
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 6082 c.843G>A synonymous_variant 0.32
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.53
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9785 c.2484G>A synonymous_variant 0.29
fgd1 490991 c.212delG frameshift_variant 0.15
mshA 575379 p.Gly11Val missense_variant 0.14
rpoB 759744 c.-63G>C upstream_gene_variant 0.12
rpoB 763317 c.3513delT frameshift_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 0.71
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775935 p.Asp849Val missense_variant 0.17
mmpL5 777292 p.Ala397Ser missense_variant 0.4
mmpL5 777882 c.581_598delCCGATCAGCAGCAGGCCG disruptive_inframe_deletion 0.17
mmpL5 777904 p.Val193Ile missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305050 p.Thr707Met missense_variant 0.18
fbiC 1305190 p.Ala754Pro missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473507 n.-151C>T upstream_gene_variant 0.18
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.36
rrl 1476007 n.2350T>G non_coding_transcript_exon_variant 1.0
rrl 1476606 n.2951dupC non_coding_transcript_exon_variant 0.12
fabG1 1673587 p.Gly50* stop_gained 0.4
rpsA 1833949 c.408T>C synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102276 p.Gly256Asp missense_variant 0.12
ndh 2102571 p.Ala158Pro missense_variant 0.1
ndh 2103225 c.-183A>C upstream_gene_variant 0.17
katG 2156404 c.-293G>A upstream_gene_variant 0.75
PPE35 2168149 p.Pro822Ser missense_variant 0.26
PPE35 2170152 p.Tyr154Cys missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726383 c.192_196delGATCG frameshift_variant 0.25
thyA 3073868 p.Thr202Ala missense_variant 0.89
thyA 3074208 c.263delG frameshift_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.75
clpC1 4038287 c.2418C>T synonymous_variant 0.57
clpC1 4039729 p.Asp326Asn missense_variant 0.43
clpC1 4040566 p.Lys47Glu missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4246161 p.Val977Leu missense_variant 0.36
aftB 4267157 c.1680G>C synonymous_variant 0.12
ethA 4327416 p.Ala20Thr missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.73