TB-Profiler result

Run: SRR5535689
Summary

Run ID: SRR5535689

Sample name:

Date: 04-04-2023 10:37:50

Number of reads: 1532371

Percentage reads mapped: 99.21

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.2 Euro-American T;H None 0.98
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
katG 2155388 c.723delC frameshift_variant 0.14 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
gyrB 7125 p.Ser629* stop_gained 0.15
gyrA 7228 c.-74C>T upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8954 p.Gln551His missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575444 p.Pro33Thr missense_variant 0.13
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760555 p.Glu250Gly missense_variant 1.0
rpoB 761280 p.Gly492Cys missense_variant 0.14
rpoC 763825 p.Glu152Asp missense_variant 0.12
rpoC 764647 c.1278C>T synonymous_variant 0.15
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765586 c.2217G>A synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776198 c.2283C>A synonymous_variant 0.16
mmpL5 776949 p.Thr511Asn missense_variant 0.12
mmpL5 777268 p.Leu405Met missense_variant 0.2
mmpL5 777550 p.Leu311Met missense_variant 0.17
mmpL5 777883 p.Gly200Ser missense_variant 0.15
mmpL5 777884 c.597C>A synonymous_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800787 c.-22C>A upstream_gene_variant 0.15
fbiC 1302920 c.-11G>A upstream_gene_variant 1.0
fbiC 1305126 c.2196T>C synonymous_variant 0.11
Rv1258c 1406725 p.Gln206Lys missense_variant 0.17
embR 1416603 p.Ala249Thr missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472923 n.1078G>T non_coding_transcript_exon_variant 0.18
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.29
rrl 1473772 n.115C>A non_coding_transcript_exon_variant 0.14
rrl 1473868 n.211C>T non_coding_transcript_exon_variant 1.0
rrl 1474908 n.1251G>A non_coding_transcript_exon_variant 0.2
rrl 1476180 n.2523C>A non_coding_transcript_exon_variant 0.5
inhA 1673475 c.-727A>G upstream_gene_variant 0.13
inhA 1675011 c.810G>T stop_lost&splice_region_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918150 p.Val71Phe missense_variant 0.14
ndh 2102750 p.Cys98Phe missense_variant 0.15
katG 2154298 p.Pro605Gln missense_variant 0.14
katG 2154845 p.Val423Ile missense_variant 0.12
PPE35 2169682 p.Gly311* stop_gained 0.2
Rv1979c 2222178 c.987G>A synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290108 c.-867C>A upstream_gene_variant 0.12
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518614 p.Pro167Gln missense_variant 0.2
eis 2715550 c.-218G>T upstream_gene_variant 0.2
ahpC 2726264 c.72C>A synonymous_variant 0.13
ahpC 2726540 c.348C>T synonymous_variant 0.22
ahpC 2726611 p.Pro140His missense_variant 0.13
folC 2746277 p.Asp441Gly missense_variant 1.0
pepQ 2860212 c.207C>A synonymous_variant 0.13
Rv2752c 3066207 c.-16A>C upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087725 c.906C>A synonymous_variant 0.13
Rv3083 3448975 c.472C>A synonymous_variant 0.15
Rv3083 3449179 p.Ile226Val missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640479 c.-64G>T upstream_gene_variant 0.12
fbiA 3640619 p.Gly26Val missense_variant 0.13
fbiB 3642772 p.Asp413Gly missense_variant 0.25
embC 4240690 c.828G>T synonymous_variant 0.21
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4248868 c.2355G>T synonymous_variant 0.12
aftB 4267404 p.Pro478Leu missense_variant 0.18
ethR 4327072 c.-477G>T upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0