TB-Profiler result

Run: SRR3732572
Summary

Run ID: SRR3732572

Sample name:

Date: 04-04-2023 05:35:44

Number of reads: 1098622

Percentage reads mapped: 99.54

Strain: lineage4.1.2.1

Drug-resistance: Sensitive

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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 1.0
lineage4.1.2 Euro-American T;H None 1.0
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
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 5661 p.Arg141Leu missense_variant 0.18
gyrB 5910 p.Ser224Ile missense_variant 0.17
gyrA 6418 c.-884C>A upstream_gene_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7442 c.141G>T synonymous_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8625 p.Arg442Ser missense_variant 0.12
gyrA 8632 p.Ala444Asp missense_variant 0.13
gyrA 9165 p.Tyr622His missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9333 p.Gly678Trp missense_variant 0.22
fgd1 490670 c.-113G>T upstream_gene_variant 0.22
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 575830 c.483C>T synonymous_variant 0.22
mshA 576025 c.678G>A synonymous_variant 0.22
ccsA 620458 p.Gly190Cys missense_variant 0.17
ccsA 620508 c.618A>G synonymous_variant 0.17
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761703 p.Gly633Cys missense_variant 0.15
rpoB 762320 c.2514C>T synonymous_variant 0.13
rpoC 763079 c.-291C>T upstream_gene_variant 0.2
rpoC 764350 p.Met327Ile missense_variant 0.22
rpoC 764379 p.Thr337Met missense_variant 0.18
rpoC 764812 c.1443C>A synonymous_variant 0.17
rpoC 765149 p.Gly594* stop_gained 0.17
rpoC 765392 p.Glu675* stop_gained 0.22
rpoC 765400 c.2031G>T synonymous_variant 0.22
rpoC 765831 c.2465dupG frameshift_variant 0.18
rpoC 767092 c.3723C>A synonymous_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775828 p.Gly885Trp missense_variant 0.2
mmpL5 775942 p.Gly847Ser missense_variant 0.18
mmpL5 777157 c.1324C>A synonymous_variant 0.12
mmpL5 778066 p.Ala139Thr missense_variant 0.14
mmpR5 778190 c.-800G>T upstream_gene_variant 0.17
mmpR5 778310 c.-680T>A upstream_gene_variant 0.15
mmpR5 778313 c.-677G>T upstream_gene_variant 0.17
mmpL5 778861 c.-381G>T upstream_gene_variant 0.4
mmpL5 778998 c.-518G>T upstream_gene_variant 0.18
mmpR5 779126 p.Cys46Phe missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800868 p.Ser20Arg missense_variant 0.17
rplC 800884 p.Val26Leu missense_variant 0.18
rplC 801172 p.Gly122Cys missense_variant 0.14
fbiC 1303256 p.Thr109Asn missense_variant 0.2
fbiC 1303737 p.Glu269Asp missense_variant 0.18
fbiC 1304852 p.Gly641Val missense_variant 0.18
Rv1258c 1407477 c.-137C>A upstream_gene_variant 0.12
embR 1416892 c.456C>T synonymous_variant 0.14
rrs 1472405 n.560C>A non_coding_transcript_exon_variant 0.67
rrl 1474301 n.644G>A non_coding_transcript_exon_variant 0.67
rrl 1476208 n.2551C>T non_coding_transcript_exon_variant 1.0
rrl 1476299 n.2642C>A non_coding_transcript_exon_variant 0.5
fabG1 1673903 p.Ala155Asp missense_variant 0.22
inhA 1674629 p.Ser143Phe missense_variant 0.22
rpsA 1833395 c.-147C>A upstream_gene_variant 0.29
rpsA 1833768 p.Pro76His missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102130 p.Val305Leu missense_variant 0.12
ndh 2102323 c.720C>T synonymous_variant 0.25
katG 2153955 p.Lys719Asn missense_variant 0.2
PPE35 2167878 p.Ser912Ile missense_variant 0.2
PPE35 2168228 c.2385C>A synonymous_variant 0.33
PPE35 2168604 p.Pro670His missense_variant 0.67
PPE35 2168623 p.Ala664Thr missense_variant 0.67
PPE35 2168642 c.1971C>T synonymous_variant 0.67
PPE35 2169910 p.Asn235Tyr missense_variant 0.33
Rv1979c 2222563 p.Ser201Ile missense_variant 0.17
Rv1979c 2223187 c.-23C>A upstream_gene_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288873 c.369C>G synonymous_variant 0.11
pncA 2289946 c.-705G>T upstream_gene_variant 0.14
kasA 2517951 c.-164G>T upstream_gene_variant 0.18
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2715439 c.-107G>A upstream_gene_variant 0.15
pepQ 2859587 p.Arg278Ser missense_variant 0.12
pepQ 2860188 c.231C>T synonymous_variant 0.2
ribD 2986936 p.Asp33Val missense_variant 0.22
Rv2752c 3065397 c.795G>A synonymous_variant 0.29
Rv2752c 3066125 p.Gly23Cys missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087182 p.Gln121His missense_variant 0.25
Rv3083 3448959 p.Asp152Glu missense_variant 0.15
Rv3083 3449731 p.Leu410Met missense_variant 0.22
Rv3083 3449901 p.Tyr466* stop_gained 0.17
fprA 3473885 c.-122G>T upstream_gene_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474165 c.159C>G synonymous_variant 0.29
fprA 3474533 p.Thr176Asn missense_variant 0.13
fprA 3475320 c.1314G>T synonymous_variant 0.18
whiB7 3568613 p.Gly23Cys missense_variant 0.17
whiB7 3568751 c.-72C>T upstream_gene_variant 0.18
whiB7 3568800 c.-121C>A upstream_gene_variant 0.18
Rv3236c 3612687 p.Gly144Ser missense_variant 0.29
Rv3236c 3612846 p.Pro91Ser missense_variant 1.0
fbiA 3640588 p.Leu16Met missense_variant 0.4
fbiB 3642397 p.Ala288Asp missense_variant 0.33
fbiB 3642521 c.987C>T synonymous_variant 0.2
alr 3841438 c.-18A>G upstream_gene_variant 0.25
alr 3841546 c.-126C>A upstream_gene_variant 0.17
ddn 3986810 c.-34C>A upstream_gene_variant 0.67
ddn 3986840 c.-4C>A upstream_gene_variant 0.67
ddn 3987183 p.Ala114Thr missense_variant 0.25
clpC1 4038230 c.2475G>A synonymous_variant 0.22
clpC1 4038249 p.Thr819Asn missense_variant 0.29
clpC1 4039999 p.Gly236Cys missense_variant 0.18
clpC1 4040299 p.Gln136Lys missense_variant 0.33
panD 4044004 p.Met93Thr missense_variant 0.2
embC 4240229 c.367C>T synonymous_variant 0.25
embC 4240476 p.Ala205Val missense_variant 0.18
embC 4241282 p.Ala474Ser missense_variant 0.13
embC 4241401 p.Phe513Leu missense_variant 0.14
embC 4241939 p.Pro693Thr missense_variant 0.25
embA 4242541 c.-692C>A upstream_gene_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4246215 p.Glu995* stop_gained 0.18
embB 4248269 p.Met586Leu missense_variant 0.2
embB 4249502 p.Gln997Lys missense_variant 0.22
aftB 4267036 p.Arg601Ser missense_variant 0.17
aftB 4268048 c.789G>T synonymous_variant 0.33
aftB 4268267 c.570G>T synonymous_variant 0.14
ubiA 4269706 p.Gly43Val missense_variant 0.14
ubiA 4269733 p.Ala34Val missense_variant 0.17
ethA 4326402 p.Gly358Arg missense_variant 0.14
ethR 4326625 c.-924G>T upstream_gene_variant 0.14
ethR 4326883 c.-666C>A upstream_gene_variant 0.15
ethA 4327698 c.-225C>A upstream_gene_variant 0.17
ethR 4327977 p.Gln143His missense_variant 0.14
ethR 4328089 p.Arg181Trp missense_variant 0.2
whiB6 4338437 p.Val29Phe missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407552 c.651G>A synonymous_variant 0.13
gid 4408442 c.-240G>T upstream_gene_variant 0.17