TB-Profiler result

Run: SRR4034600
Summary

Run ID: SRR4034600

Sample name:

Date: 04-04-2023 06:54:44

Number of reads: 1258283

Percentage reads mapped: 99.7

Strain: lineage4.3.3;lineage4.1.1.3

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 0.69
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.28
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.74
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.3
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 8040 p.Gly247Ser missense_variant 0.47
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 762006 p.Arg734Ser missense_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 0.8
rpoC 765150 p.Gly594Glu missense_variant 0.29
rpoC 766904 p.Ser1179Pro missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777361 p.Ala374Ser missense_variant 0.14
mmpL5 778600 c.-120C>T upstream_gene_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.74
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169550 c.1062delC frameshift_variant 0.11
Rv1979c 2223051 p.Glu38Asp missense_variant 0.8
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.64
pepQ 2860146 c.273C>T synonymous_variant 0.12
Rv2752c 3065824 p.Pro123Leu missense_variant 0.76
thyA 3073868 p.Thr202Ala missense_variant 0.64
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448583 c.84delC frameshift_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612753 p.Ala122Thr missense_variant 0.25
clpC1 4038287 c.2418C>T synonymous_variant 0.54
clpC1 4038857 c.1848C>A synonymous_variant 0.2
clpC1 4039949 c.756G>A synonymous_variant 0.41
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.11
embA 4243762 p.Leu177Pro missense_variant 0.11
embB 4249408 c.2895G>A synonymous_variant 0.42
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 0.29
gid 4408156 p.Leu16Arg missense_variant 0.78