TB-Profiler result

Run: ERR2229129
Summary

Run ID: ERR2229129

Sample name:

Date: 31-03-2023 16:42:41

Number of reads: 519443

Percentage reads mapped: 99.45

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
tlyA 1918388 c.451delG frameshift_variant 0.17 capreomycin
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 8924 c.1623C>A synonymous_variant 0.14
gyrA 9297 p.Ser666Thr missense_variant 0.17
mshA 576108 p.Ala254Gly missense_variant 0.29
ccsA 620703 c.813G>A synonymous_variant 0.25
rpoB 760571 c.765G>A synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776303 c.2178G>C synonymous_variant 0.22
mmpL5 776842 p.Ala547Thr missense_variant 0.4
mmpL5 778090 p.Gly131Trp missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800983 p.Pro59Thr missense_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304673 c.1743C>T synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673171 c.-269T>C upstream_gene_variant 0.2
fabG1 1673380 c.-60C>G upstream_gene_variant 0.4
rpsA 1834684 c.1143C>T synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102453 p.Leu197* stop_gained 0.18
katG 2155115 p.Leu333Phe missense_variant 0.17
PPE35 2167865 c.2748G>C synonymous_variant 0.14
PPE35 2167868 c.2745A>C synonymous_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.41
PPE35 2170053 p.Thr187Ser missense_variant 0.41
PPE35 2170147 p.Ser156Ala missense_variant 0.12
Rv1979c 2222215 p.Val317Asp missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2987369 c.531G>T synonymous_variant 0.22
Rv2752c 3065999 p.Arg65Cys missense_variant 0.14
fbiD 3339364 p.Pro83Ala missense_variant 0.11
fbiD 3339474 c.357A>T synonymous_variant 0.18
fbiD 3339483 c.366A>G synonymous_variant 0.18
fbiB 3641628 p.Ala32Thr missense_variant 0.17
rpoA 3878314 p.Thr65Met missense_variant 0.13
ddn 3986868 p.Leu9Met missense_variant 0.15
clpC1 4039526 c.1179G>C synonymous_variant 0.17
clpC1 4039530 p.Asp392Ala missense_variant 0.22
clpC1 4040144 c.561G>C synonymous_variant 0.14
clpC1 4040897 c.-193G>A upstream_gene_variant 0.17
embA 4242499 c.-734G>A upstream_gene_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243924 p.Arg231His missense_variant 0.33
embA 4244734 p.Arg501His missense_variant 0.5
embB 4247028 p.Leu172Arg missense_variant 0.17
embB 4249267 c.2754C>T synonymous_variant 0.22
ethR 4326577 c.-972G>T upstream_gene_variant 0.12
ethA 4327764 c.-291C>A upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408122 c.81G>A synonymous_variant 0.17
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0