TB-Profiler result

Run: ERR2229595
Summary

Run ID: ERR2229595

Sample name:

Date: 31-03-2023 17:21:58

Number of reads: 1536882

Percentage reads mapped: 99.42

Strain: lineage4.8

Drug-resistance: RR-TB

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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
rpoB 761143 p.Lys446Thr missense_variant 0.18 rifampicin
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
mshA 575412 p.Glu22Ala missense_variant 0.33
mshA 576775 c.1428C>T synonymous_variant 0.2
rpoB 761152 p.Leu449Gln missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777119 p.His454Gln missense_variant 0.17
mmpL5 777122 c.1359C>T synonymous_variant 0.17
mmpL5 777128 c.1353A>G synonymous_variant 0.19
mmpL5 779184 c.-704C>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.2
PPE35 2169281 c.1332T>G synonymous_variant 0.2
PPE35 2169902 p.Leu237Phe missense_variant 0.24
PPE35 2169910 p.Asn235Tyr missense_variant 0.22
PPE35 2170048 p.Leu189Val missense_variant 0.51
PPE35 2170053 p.Thr187Ser missense_variant 0.55
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746628 p.Asp324Val missense_variant 0.17
Rv2752c 3064830 c.1362C>G synonymous_variant 0.17
thyX 3067510 p.Leu146Met missense_variant 0.12
fbiD 3339734 p.Ala206Gly missense_variant 0.5
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.2
Rv3236c 3612521 p.Ser199Trp missense_variant 0.11
alr 3841546 c.-126C>A upstream_gene_variant 0.28
rpoA 3878560 c.-53C>T upstream_gene_variant 0.4
clpC1 4038442 p.Ala755Thr missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245553 p.Pro774His missense_variant 0.13
embB 4246544 p.Thr11Pro missense_variant 0.4
embB 4246548 p.Pro12Gln missense_variant 0.4
embB 4246555 c.42G>C synonymous_variant 0.6
embB 4246556 p.Ala15Pro missense_variant 0.6
embB 4246584 p.Arg24Pro missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0