TB-Profiler result

Run: SRR5535921
Summary

Run ID: SRR5535921

Sample name:

Date: 04-04-2023 10:44:54

Number of reads: 1712530

Percentage reads mapped: 99.03

Strain: lineage4.4.1.1

Drug-resistance: MDR-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
lineage4.4 Euro-American S;T None 0.99
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans None 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 761155 p.Ser450Trp missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.95 isoniazid
embB 4248003 p.Gln497Arg 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
gyrB 5045 c.-195C>A upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9138 p.Gln613Glu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576073 c.726C>A synonymous_variant 0.17
rpoC 764628 p.Lys420Arg missense_variant 0.19
rpoC 764854 c.1485G>T synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777416 c.1065G>T synonymous_variant 1.0
mmpL5 777424 p.Leu353Met missense_variant 0.17
mmpL5 778131 p.Gln117Arg missense_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303555 p.Pro209Ser missense_variant 0.13
embR 1416423 c.925C>A synonymous_variant 0.17
embR 1416859 c.489C>A synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472452 n.607G>T non_coding_transcript_exon_variant 0.15
rrl 1475032 n.1375G>T non_coding_transcript_exon_variant 0.4
rpsA 1833909 p.Asp123Ala missense_variant 0.92
rpsA 1834922 p.Gly461Cys missense_variant 0.17
tlyA 1917925 c.-15A>G upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 0.94
katG 2154724 p.Arg463Leu missense_variant 0.17
katG 2155817 p.Gly99Trp missense_variant 0.17
PPE35 2168479 p.Thr712Pro missense_variant 0.93
PPE35 2169520 p.Gly365Cys missense_variant 0.17
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2222070 p.Leu365Phe missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288952 p.Gly97Asn missense_variant 0.9
kasA 2519016 p.Ser301Leu missense_variant 0.15
eis 2714814 c.519C>A synonymous_variant 0.14
eis 2715520 c.-188C>A upstream_gene_variant 0.14
ahpC 2726285 c.93C>A synonymous_variant 0.17
ribD 2987163 c.325C>A synonymous_variant 0.12
Rv2752c 3064814 c.1369_1377delGTCGGCGAT conservative_inframe_deletion 1.0
Rv2752c 3067081 c.-890T>C upstream_gene_variant 0.12
Rv2752c 3067161 c.-970C>A upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 0.94
ald 3086864 c.45G>T synonymous_variant 0.16
fbiD 3339684 c.567C>A synonymous_variant 0.15
Rv3083 3448608 c.105G>A synonymous_variant 1.0
Rv3083 3448975 c.472C>A synonymous_variant 0.12
Rv3083 3449234 p.Arg244His missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568779 c.-100T>C upstream_gene_variant 1.0
Rv3236c 3612291 p.Leu276Met missense_variant 0.12
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
Rv3236c 3612871 p.Phe82Leu missense_variant 0.15
Rv3236c 3613222 c.-106T>C upstream_gene_variant 0.15
fbiA 3640468 c.-75G>C upstream_gene_variant 0.12
fbiA 3640579 p.Ala13Pro missense_variant 0.12
ddn 3986667 c.-177C>A upstream_gene_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242967 c.-266C>A upstream_gene_variant 0.23
embA 4243185 c.-48G>T upstream_gene_variant 0.2
embB 4249719 p.Thr1069Asn missense_variant 0.15
aftB 4267831 p.Gly336Cys missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407986 p.Gly73Arg missense_variant 1.0