TB-Profiler result

Run: ERR2245276
Summary

Run ID: ERR2245276

Sample name:

Date: 31-03-2023 17:36:52

Number of reads: 1953858

Percentage reads mapped: 98.82

Strain: lineage3.1

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
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 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
tlyA 1918739 c.803delC frameshift_variant 0.4 capreomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4327222 c.251delA frameshift_variant 0.13 ethionamide
gid 4407796 p.Ser136* stop_gained 0.17 streptomycin
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 5840 p.Asn201Tyr missense_variant 0.4
gyrB 6053 p.His272Tyr missense_variant 0.33
gyrB 6421 p.His394Gln missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9557 c.2256G>T synonymous_variant 0.29
gyrA 9774 p.Asp825Tyr missense_variant 0.38
fgd1 491326 p.Ala182Ser missense_variant 0.29
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575254 c.-94C>T upstream_gene_variant 0.2
mshA 575972 p.Glu209Lys missense_variant 0.33
mshA 576108 p.Ala254Gly missense_variant 0.35
ccsA 620679 c.789C>A synonymous_variant 0.25
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760631 c.825G>T synonymous_variant 0.22
rpoB 761587 p.Asp594Val missense_variant 0.25
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763796 p.Met143Leu missense_variant 0.25
rpoC 764101 c.732C>T synonymous_variant 0.22
rpoC 764208 p.Val280Gly missense_variant 0.29
rpoC 764456 p.Pro363Thr missense_variant 0.22
rpoC 764610 p.Arg414Gln missense_variant 0.2
rpoC 764866 c.1497C>T synonymous_variant 0.25
rpoC 765545 p.Arg726Ser missense_variant 0.15
rpoC 766415 p.His1016Tyr missense_variant 0.4
rpoC 766795 p.Tyr1142* stop_gained 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776711 p.His590Gln missense_variant 0.22
mmpL5 777676 p.Leu269Met missense_variant 0.33
mmpR5 778451 c.-539C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781404 c.-156G>T upstream_gene_variant 0.5
rplC 801113 p.Thr102Asn missense_variant 0.2
fbiC 1303391 p.Arg154Leu missense_variant 0.5
fbiC 1303576 p.Glu216* stop_gained 0.2
fbiC 1304270 p.Val447Gly missense_variant 0.67
fbiC 1304707 p.Val593Ile missense_variant 0.5
fbiC 1305177 c.2249dupC frameshift_variant 0.22
fbiC 1305197 p.Ala756Val missense_variant 0.12
fbiC 1305361 p.Leu811Met missense_variant 0.17
Rv1258c 1406599 p.Pro248Thr missense_variant 0.22
Rv1258c 1407266 c.75C>A synonymous_variant 0.4
embR 1416493 c.855C>A synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476461 n.2804A>G non_coding_transcript_exon_variant 0.17
rrl 1476736 n.3079A>C non_coding_transcript_exon_variant 0.18
fabG1 1674091 p.Ala218Ser missense_variant 0.22
inhA 1674997 p.Thr266Pro missense_variant 0.29
rpsA 1833982 p.Phe147Leu missense_variant 0.18
rpsA 1834039 c.498C>A synonymous_variant 0.17
rpsA 1834735 c.1194C>T synonymous_variant 0.18
rpsA 1834806 p.Glu422Val missense_variant 0.33
rpsA 1834822 p.Met427Ile missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918428 c.489G>T synonymous_variant 0.2
tlyA 1918607 p.Val223Gly missense_variant 0.67
ndh 2102054 p.Pro330Leu missense_variant 0.17
ndh 2102128 c.915G>T synonymous_variant 0.67
ndh 2102733 p.Leu104Ile missense_variant 0.18
katG 2154489 c.1623C>A synonymous_variant 0.22
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154871 p.Lys414Arg missense_variant 0.19
katG 2155033 p.Gly360Asp missense_variant 0.29
katG 2155706 p.Pro136Thr missense_variant 0.33
katG 2156356 c.-245G>T upstream_gene_variant 0.27
katG 2156415 c.-304C>G upstream_gene_variant 0.14
PPE35 2167740 p.Thr958Ile missense_variant 0.29
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168843 c.1770G>A synonymous_variant 0.17
PPE35 2169049 p.Ile522Phe missense_variant 0.15
PPE35 2169125 c.1488T>A synonymous_variant 0.15
PPE35 2169237 p.Asp459Val missense_variant 0.17
PPE35 2169417 p.Thr399Lys missense_variant 0.25
PPE35 2169838 p.Ile259Leu missense_variant 0.13
Rv1979c 2222113 p.Val351Gly missense_variant 0.25
Rv1979c 2222371 p.Ala265Glu missense_variant 0.2
Rv1979c 2223126 p.Lys13Asn missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289352 c.-112delG upstream_gene_variant 0.25
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518307 p.Lys65* stop_gained 0.29
kasA 2518531 c.417G>A synonymous_variant 0.22
eis 2714410 p.Arg308Leu missense_variant 0.29
ahpC 2726061 c.-132G>T upstream_gene_variant 0.15
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746395 p.Val402Phe missense_variant 0.4
pepQ 2859751 p.Gly223Val missense_variant 0.25
pepQ 2859811 p.Pro203Leu missense_variant 0.5
pepQ 2860296 c.123C>A synonymous_variant 0.2
ribD 2987213 c.375C>A synonymous_variant 0.67
ribD 2987541 c.703C>T synonymous_variant 0.67
thyX 3067276 p.Pro224Thr missense_variant 0.5
thyX 3067533 p.Ala138Val missense_variant 0.29
thyX 3068065 c.-120G>C upstream_gene_variant 0.29
thyA 3074235 c.237C>A synonymous_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087394 p.Ala192Val missense_variant 0.18
fbiD 3339171 c.54C>A synonymous_variant 0.17
Rv3083 3449258 p.Arg252Gln missense_variant 1.0
Rv3083 3449841 c.1338C>A synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474052 p.Phe16Ile missense_variant 0.4
fprA 3474320 p.Gly105Asp missense_variant 0.18
fprA 3474634 p.Leu210Val missense_variant 0.2
fprA 3475110 c.1104C>T synonymous_variant 0.5
fprA 3475250 p.Pro415Arg missense_variant 0.33
Rv3236c 3612581 p.Leu179Arg missense_variant 0.33
Rv3236c 3612637 p.Phe160Leu missense_variant 0.4
fbiB 3641912 p.Asp126Glu missense_variant 0.29
fbiB 3642666 p.Gly378Arg missense_variant 0.4
fbiB 3642673 p.Ala380Asp missense_variant 0.33
fbiB 3642728 c.1194C>T synonymous_variant 0.4
alr 3840631 p.Pro264Ser missense_variant 0.29
alr 3840688 p.Asp245Tyr missense_variant 0.22
rpoA 3877935 p.Lys191Asn missense_variant 0.15
ddn 3987061 p.Val73Gly missense_variant 0.29
clpC1 4038212 p.Asp831Glu missense_variant 0.4
clpC1 4039166 p.Glu513Asp missense_variant 0.15
clpC1 4039626 p.Lys360Met missense_variant 0.33
clpC1 4040249 p.Glu152Asp missense_variant 0.33
clpC1 4040262 p.Lys148Met missense_variant 0.4
clpC1 4040457 p.Arg83Leu missense_variant 0.15
embC 4239879 p.Ala6Gly missense_variant 0.27
embC 4240172 p.Val104Met missense_variant 1.0
embC 4240239 p.Ala126Asp missense_variant 0.25
embC 4241187 p.Gly442Asp missense_variant 0.4
embC 4241562 p.Arg567His missense_variant 1.0
embC 4241679 p.Val606Gly missense_variant 0.33
embC 4242075 p.Arg738Gln missense_variant 0.92
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242851 p.Phe997Ile missense_variant 0.29
embA 4243212 c.-21C>A upstream_gene_variant 0.25
embA 4243235 c.3G>A synonymous_variant 0.29
embA 4243253 p.Glu7Asp missense_variant 0.33
embA 4243448 c.216C>A synonymous_variant 0.67
embA 4244715 p.Trp495Arg missense_variant 0.29
embA 4244781 p.Arg517Ser missense_variant 0.33
embA 4244989 p.Ala586Val missense_variant 0.2
embA 4245160 p.Ser643Ile missense_variant 0.15
embB 4247024 p.Pro171Ala missense_variant 1.0
embB 4247438 p.Val309Phe missense_variant 0.15
embB 4247458 p.Tyr315* stop_gained 0.14
embB 4247625 p.Pro371His missense_variant 0.25
embB 4248897 p.Glu795Val missense_variant 0.17
embB 4249586 p.Thr1025Ser missense_variant 0.25
aftB 4268619 p.Val73Gly missense_variant 0.5
aftB 4268689 p.Asn50Asp missense_variant 0.33
ubiA 4269230 p.Thr202Ala missense_variant 0.25
aftB 4269348 c.-512C>A upstream_gene_variant 0.14
ubiA 4269781 p.Val18Gly missense_variant 0.29
ubiA 4269793 p.Val14Gly missense_variant 0.22
ubiA 4269959 c.-126C>A upstream_gene_variant 0.33
ethA 4327543 c.-70C>A upstream_gene_variant 0.22
ethR 4328041 p.Thr165Pro missense_variant 0.27
ethA 4328436 c.-963G>T upstream_gene_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407553 p.Arg217Gln missense_variant 0.4
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408321 c.-119C>T upstream_gene_variant 0.33
gid 4408396 c.-194G>T upstream_gene_variant 0.22