TB-Profiler result

Run: SRR6046130
Summary

Run ID: SRR6046130

Sample name:

Date: 04-04-2023 12:11:39

Number of reads: 766949

Percentage reads mapped: 96.45

Strain: lineage4.7;lineage4.2.1.1

Drug-resistance: HR-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 0.78
lineage4.7 Euro-American (mainly T) T1;T5 None 0.27
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.75
lineage4.2.1.1 Euro-American (TUR) H3;H4 None 0.76
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
rpsL 781687 p.Lys43Arg missense_variant 0.66 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.82 isoniazid
pncA 2288952 p.Gly97Val missense_variant 0.13 pyrazinamide
embB 4247325 p.Ala271Val missense_variant 0.11 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 7446 p.Lys49Glu missense_variant 0.1
gyrA 7585 p.Ser95Thr missense_variant 0.79
gyrA 8432 c.1131C>G synonymous_variant 0.42
gyrA 9304 p.Gly668Asp missense_variant 0.79
gyrA 9513 p.Glu738* stop_gained 0.11
gyrA 9567 p.Asp756Asn missense_variant 0.13
fgd1 490995 c.213C>T synonymous_variant 0.13
mshA 576751 p.Lys468Asn missense_variant 0.29
rpoB 761784 p.Thr660Ala missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777315 p.Trp389Leu missense_variant 0.23
mmpL5 777451 p.Val344Leu missense_variant 0.89
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406962 p.Met127Val missense_variant 0.12
atpE 1461083 c.39T>G synonymous_variant 0.3
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1674076 p.Thr213Pro missense_variant 0.26
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 0.67
PPE35 2170048 p.Leu189Val missense_variant 0.22
PPE35 2170053 p.Thr187Ser missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290079 c.-838T>C upstream_gene_variant 0.75
kasA 2518852 p.Met246Ile missense_variant 0.13
ahpC 2726338 p.Val49Gly missense_variant 0.36
ahpC 2726341 p.Val50Gly missense_variant 0.29
folC 2746745 p.Val285Gly missense_variant 0.33
folC 2746964 p.Ile212Thr missense_variant 0.12
pepQ 2859918 c.501A>T synonymous_variant 0.13
pepQ 2860434 c.-16A>G upstream_gene_variant 0.11
thyX 3067407 p.Glu180Gly missense_variant 0.12
thyX 3068022 c.-77C>G upstream_gene_variant 0.23
ald 3086742 c.-78A>C upstream_gene_variant 0.74
ald 3086788 c.-32T>C upstream_gene_variant 0.72
Rv3083 3448484 c.-20T>G upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.72
Rv3236c 3612255 p.Val288Phe missense_variant 0.17
fbiB 3642290 c.756T>C synonymous_variant 0.15
fbiB 3642496 p.Leu321Pro missense_variant 0.11
fbiB 3642772 p.Asp413Ala missense_variant 0.4
fbiB 3642848 c.1314G>A synonymous_variant 0.21
ddn 3986975 c.132T>C synonymous_variant 0.31
ddn 3987092 p.Glu83Asp missense_variant 0.8
clpC1 4040320 p.Ala129Ser missense_variant 0.12
embC 4240865 p.Ala335Pro missense_variant 0.38
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244354 c.1122G>A synonymous_variant 0.17
embA 4244905 p.Val558Gly missense_variant 0.22
embB 4249732 c.3219C>G synonymous_variant 0.28
ethA 4326453 p.Ala341Thr missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408213 c.-11C>T upstream_gene_variant 0.69