TB-Profiler result

Run: SRR029823
Summary

Run ID: SRR029823

Sample name:

Date: 02-04-2023 14:14:05

Number of reads: 2753654

Percentage reads mapped: 52.29

Strain: lineage4.2.2.2

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 0.96
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.96
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.95
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 0.9 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.77 isoniazid, ethionamide
pncA 2289252 c.-11A>G upstream_gene_variant 0.85 pyrazinamide
ahpC 2726145 c.-48G>A upstream_gene_variant 0.95 isoniazid
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 8540 c.1239C>A synonymous_variant 0.15
gyrA 8688 p.Ala463Ser missense_variant 0.94
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575357 p.Val4Leu missense_variant 0.29
mshA 576077 c.730C>T synonymous_variant 0.87
ccsA 619802 c.-89G>T upstream_gene_variant 0.2
ccsA 619906 p.Val6Leu missense_variant 0.13
ccsA 619925 p.Arg12Leu missense_variant 0.18
ccsA 619999 p.Ala37Thr missense_variant 0.67
rpoB 760516 p.Trp237Leu missense_variant 0.17
rpoB 761489 c.1683G>A synonymous_variant 0.95
rpoC 763886 c.517C>A synonymous_variant 0.2
rpoC 763930 p.Glu187Asp missense_variant 0.29
rpoC 765150 p.Gly594Glu missense_variant 0.15
rpoC 766583 p.Gly1072Cys missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801200 p.Gly131Val missense_variant 0.18
fbiC 1305217 p.His763Asn missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471709 n.-137G>T upstream_gene_variant 0.14
rrs 1471728 n.-118A>G upstream_gene_variant 0.12
rrs 1472268 n.423G>T non_coding_transcript_exon_variant 0.14
rrl 1473908 n.251C>A non_coding_transcript_exon_variant 0.15
rrl 1475852 n.2195C>A non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918167 c.228G>T synonymous_variant 0.2
katG 2154610 p.Pro501Leu missense_variant 0.2
katG 2155306 p.Gly269Val missense_variant 0.18
katG 2155879 p.Arg78Leu missense_variant 0.15
katG 2156377 c.-266C>G upstream_gene_variant 0.11
PPE35 2170293 p.Pro107Leu missense_variant 0.2
PPE35 2170348 p.Gln89Lys missense_variant 0.67
PPE35 2170350 p.Thr88Asn missense_variant 0.67
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519326 p.Phe404Leu missense_variant 0.2
eis 2715228 c.105C>A synonymous_variant 0.22
pepQ 2859637 p.Arg261Leu missense_variant 0.22
pepQ 2859657 c.762C>T synonymous_variant 0.15
ribD 2987414 c.576C>G synonymous_variant 0.25
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.94
thyX 3067361 p.Phe195Leu missense_variant 0.2
ald 3086742 c.-78A>C upstream_gene_variant 0.97
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087308 c.489G>T synonymous_variant 0.33
fbiD 3339075 c.-43C>A upstream_gene_variant 0.17
Rv3083 3449420 p.Phe306Ser missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474401 p.Tyr132Cys missense_variant 0.12
fprA 3475362 c.1356G>T synonymous_variant 0.33
fprA 3475368 c.1362G>T synonymous_variant 0.29
Rv3236c 3611975 p.Ala381Val missense_variant 0.18
fbiB 3642708 p.Gly392Trp missense_variant 0.29
fbiB 3642792 p.Pro420Thr missense_variant 0.29
fbiB 3642801 p.Ala423Ser missense_variant 0.22
alr 3840746 p.Gln225His missense_variant 0.88
alr 3840978 p.Thr148Asn missense_variant 0.14
clpC1 4039509 p.Ala399Glu missense_variant 0.15
clpC1 4039518 p.Pro396His missense_variant 0.17
embC 4239846 c.-17C>A upstream_gene_variant 0.29
embC 4240369 c.507C>G synonymous_variant 0.12
embC 4240590 p.Ala243Val missense_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243481 c.249C>A synonymous_variant 0.2
embA 4243981 p.Ser250Ile missense_variant 0.22
embA 4244479 p.Thr416Lys missense_variant 0.17
embB 4246635 p.Ser41* stop_gained 0.18
embB 4248556 c.2043C>A synonymous_variant 0.18
embB 4248562 c.2049G>A synonymous_variant 0.2
aftB 4267657 p.Gly394Cys missense_variant 0.15
aftB 4268908 c.-72C>A upstream_gene_variant 0.18
ethA 4326203 p.Ser424* stop_gained 0.81
ethR 4327832 p.Ala95Asp missense_variant 0.2
ethR 4327865 p.Gly106Val missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407791 p.Ala138Pro missense_variant 0.15