TB-Profiler result

Run: SRR4033471

Summary

Run ID: SRR4033471

Sample name:

Date: 04-04-2023 06:07:11

Number of reads: 1112975

Percentage reads mapped: 99.64

Strain: lineage4.3.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
katG 2155331 p.Glu261Lys missense_variant 0.18 isoniazid
ethA 4327257 p.Gln73* stop_gained 0.15 ethionamide
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 5111 c.-129C>A upstream_gene_variant 0.13
gyrB 5520 p.Pro94Leu missense_variant 1.0
gyrB 6455 p.Val406Ile missense_variant 0.13
gyrA 6478 c.-824G>T upstream_gene_variant 0.22
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7396 p.Ala32Val missense_variant 0.33
gyrA 7434 p.Arg45Cys missense_variant 0.25
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7823 c.522G>A synonymous_variant 0.15
gyrA 7898 c.597C>T synonymous_variant 0.25
gyrA 8055 c.754C>A synonymous_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491332 p.Tyr184His missense_variant 0.22
fgd1 491756 p.Gln325Arg missense_variant 0.18
mshA 575345 c.-3_-2insG upstream_gene_variant 0.14
mshA 575679 p.Asn111Thr missense_variant 0.14
mshA 576590 p.Arg415Trp missense_variant 0.22
ccsA 619942 p.Phe18Leu missense_variant 0.18
rpoB 760962 p.Gly386Ser missense_variant 0.18
rpoB 760969 p.Ser388* stop_gained 0.17
rpoB 760986 p.Val394Ile missense_variant 0.17
rpoB 761001 p.Thr399Ser missense_variant 0.18
rpoC 763556 p.Gly63Ser missense_variant 0.14
rpoC 763668 p.Pro100Arg missense_variant 0.17
rpoC 764141 p.Ala258Ser missense_variant 0.14
rpoC 764911 c.1542A>C synonymous_variant 0.18
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765588 p.Pro740Gln missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775650 p.Arg944Leu missense_variant 0.15
mmpL5 776130 p.Leu784Pro missense_variant 0.29
mmpL5 776148 p.Ile778Thr missense_variant 0.22
mmpL5 777284 c.1197C>T synonymous_variant 0.13
mmpL5 778122 p.Thr120Ile missense_variant 0.12
mmpR5 779096 p.Ala36Val missense_variant 0.15
rpsL 781367 c.-193G>A upstream_gene_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303566 c.636C>G synonymous_variant 0.12
fbiC 1303657 p.Arg243Cys missense_variant 0.25
fbiC 1304072 p.Thr381Ile missense_variant 0.12
fbiC 1304910 c.1980G>A synonymous_variant 0.15
Rv1258c 1407473 c.-133C>T upstream_gene_variant 0.15
embR 1416451 c.897C>T synonymous_variant 0.13
embR 1416717 c.631C>T synonymous_variant 0.13
embR 1416720 p.Gln210Lys missense_variant 0.13
embR 1417010 p.Gly113Glu missense_variant 0.13
embR 1417014 p.Leu112Val missense_variant 0.13
embR 1417220 p.Val43Gly missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrs 1472731 n.886C>G non_coding_transcript_exon_variant 0.25
rrs 1473285 n.1443delC non_coding_transcript_exon_variant 0.22
rrl 1473567 n.-91A>G upstream_gene_variant 0.5
rrl 1474153 n.496C>T non_coding_transcript_exon_variant 0.2
rrl 1475141 n.1484A>T non_coding_transcript_exon_variant 1.0
rrl 1475148 n.1491G>T non_coding_transcript_exon_variant 0.67
inhA 1674670 p.Ala157Thr missense_variant 0.13
rpsA 1834106 p.Ala189Thr missense_variant 0.22
rpsA 1834150 c.609G>T synonymous_variant 0.13
rpsA 1834860 p.Ala440Gly missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918172 p.Ala78Val missense_variant 0.13
ndh 2101913 p.Ser377Leu missense_variant 0.12
katG 2155035 c.1077C>G synonymous_variant 0.12
katG 2155053 c.1059C>T synonymous_variant 0.17
katG 2155398 c.714C>T synonymous_variant 0.15
PPE35 2168009 c.2604C>T synonymous_variant 0.13
PPE35 2168395 p.Ser740Cys missense_variant 0.18
PPE35 2168407 p.Leu736Val missense_variant 0.18
PPE35 2168582 c.2031C>T synonymous_variant 0.33
PPE35 2169474 p.Gly380Asp missense_variant 0.17
PPE35 2169765 p.Gly283Val missense_variant 0.13
PPE35 2170284 p.Val110Glu missense_variant 0.18
PPE35 2170498 p.Ala39Thr missense_variant 0.14
Rv1979c 2222677 p.Asn163Ser missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289667 c.-426C>T upstream_gene_variant 0.13
pncA 2290211 c.-970G>C upstream_gene_variant 0.13
pncA 2290216 c.-975T>C upstream_gene_variant 0.12
ahpC 2726174 c.-19T>C upstream_gene_variant 0.12
folC 2747271 p.Ile110Val missense_variant 0.13
pepQ 2860244 p.Arg59Trp missense_variant 0.14
pepQ 2860612 c.-194A>T upstream_gene_variant 0.12
Rv2752c 3065768 p.Glu142* stop_gained 0.13
Rv2752c 3065796 p.Gln132His missense_variant 0.1
Rv2752c 3066043 p.Pro50His missense_variant 0.18
Rv2752c 3066301 c.-111dupC upstream_gene_variant 0.12
thyX 3067363 p.Phe195Leu missense_variant 0.17
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074124 c.348G>C synonymous_variant 0.13
thyA 3074139 p.Gln111His missense_variant 0.17
thyA 3074181 p.Gln97His missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448415 c.-89G>C upstream_gene_variant 0.12
Rv3083 3449068 p.Ala189Thr missense_variant 0.15
Rv3083 3449809 p.Phe436Ile missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474643 c.638delG frameshift_variant 0.14
Rv3236c 3612608 p.Ala170Val missense_variant 0.14
fbiB 3642577 p.Val348Ala missense_variant 0.11
alr 3841288 p.Ile45Phe missense_variant 0.17
alr 3841350 p.Ala24Asp missense_variant 0.13
alr 3841491 c.-71A>C upstream_gene_variant 0.2
rpoA 3877803 c.705G>A synonymous_variant 0.22
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4240698 p.Ala279Gly missense_variant 0.14
embC 4242088 p.Gln742His missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248795 p.Ala761Val missense_variant 0.15
ethA 4326018 p.Pro486Ala missense_variant 0.15
ethA 4327401 p.Asp25His missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0