TB-Profiler result

Run: SRR6832685
Summary

Run ID: SRR6832685

Sample name:

Date: 04-04-2023 17:34:50

Number of reads: 2967876

Percentage reads mapped: 96.24

Strain: lineage4.2.1.1

Drug-resistance: Pre-XDR-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
lineage4.2 Euro-American H;T;LAM None 0.98
lineage4.2.1 Euro-American (TUR) H3;H4 None 1.0
lineage4.2.1.1 Euro-American (TUR) H3;H4 None 0.99
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
gyrA 7582 p.Asp94Gly missense_variant 0.98 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673432 c.-8T>C upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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
rpoB 761606 c.1800C>G synonymous_variant 0.12
rpoB 761612 c.1806G>C synonymous_variant 0.13
rpoC 763546 c.177A>G synonymous_variant 0.11
rpoC 763780 c.411C>G synonymous_variant 0.13
rpoC 763783 c.414G>C synonymous_variant 0.15
rpoC 763801 c.432C>G synonymous_variant 0.12
rpoC 763807 c.438T>C synonymous_variant 0.12
rpoC 763819 c.450G>C synonymous_variant 0.14
rpoC 763831 c.462A>G synonymous_variant 0.17
rpoC 763835 p.Ala156Met missense_variant 0.15
rpoC 764059 c.690G>C synonymous_variant 0.12
rpoC 764083 c.714A>G synonymous_variant 0.12
rpoC 764098 c.729A>G synonymous_variant 0.12
rpoC 764101 c.732C>G synonymous_variant 0.11
rpoC 764380 c.1011G>C synonymous_variant 0.12
rpoC 764381 c.1012_1013delTCinsAG synonymous_variant 0.12
rpoC 764387 c.1018_1020delTTGinsCTC synonymous_variant 0.12
rpoC 764431 c.1062G>C synonymous_variant 0.13
rpoC 764434 c.1065A>G synonymous_variant 0.13
rpoC 764446 c.1077T>C synonymous_variant 0.13
rpoC 764449 c.1080G>C synonymous_variant 0.13
rpoC 764455 c.1086G>C synonymous_variant 0.1
rpoC 764817 p.Val483Ala missense_variant 0.95
rpoC 766726 c.3357T>C synonymous_variant 0.12
rpoC 766765 c.3396A>C synonymous_variant 0.11
rpoC 766774 c.3405T>C synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777451 p.Val344Leu missense_variant 0.95
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 0.98
rpsA 1834000 c.459G>C synonymous_variant 0.14
rpsA 1834015 c.474G>C synonymous_variant 0.17
rpsA 1834021 c.480C>T synonymous_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 1.0
PPE35 2170066 p.Ala183Thr missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407973 p.Val77Ala missense_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 1.0