TB-Profiler result

Run: ERR9030302
Summary

Run ID: ERR9030302

Sample name:

Date: 02-04-2023 09:25:04

Number of reads: 1691942

Percentage reads mapped: 99.88

Strain: lineage1.1.2

Drug-resistance: MDR-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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 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
rpoB 761140 p.His445Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Asn missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.98
mshA 575423 p.Arg26Ser missense_variant 0.14
mshA 576361 c.1014C>T synonymous_variant 0.12
ccsA 619740 c.-151C>T upstream_gene_variant 0.18
rpoB 761659 p.Pro618Gln missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 763913 p.Ala182Thr missense_variant 0.14
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 766819 c.3450C>T synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777309 p.Gly391Val missense_variant 0.29
mmpL5 777360 p.Ala374Glu missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801251 p.Pro148Leu missense_variant 0.14
fbiC 1303160 p.Gly77Val missense_variant 0.22
fbiC 1304141 p.Ala404Glu missense_variant 0.13
fbiC 1304223 c.1293G>T synonymous_variant 0.5
Rv1258c 1406940 p.Arg134Leu missense_variant 0.17
Rv1258c 1407477 c.-137C>T upstream_gene_variant 0.13
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471965 n.123dupG non_coding_transcript_exon_variant 0.14
rrs 1471987 n.142G>T non_coding_transcript_exon_variant 0.2
rrl 1474888 n.1231C>A non_coding_transcript_exon_variant 0.25
rrl 1475134 n.1477G>T non_coding_transcript_exon_variant 0.2
inhA 1673550 c.-652C>T upstream_gene_variant 0.13
rpsA 1834915 c.1374G>A synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918020 c.81C>A synonymous_variant 0.27
tlyA 1918623 c.684C>T synonymous_variant 0.17
tlyA 1918633 p.Gly232Cys missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 0.95
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2170182 p.Trp144Leu missense_variant 0.13
PPE35 2170332 p.Val94* stop_gained 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288776 c.466C>T synonymous_variant 0.14
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518912 c.798G>T synonymous_variant 0.13
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726468 c.276G>A synonymous_variant 1.0
pepQ 2860056 p.Leu121Phe missense_variant 0.33
pepQ 2860592 c.-174T>C upstream_gene_variant 0.11
ribD 2987348 c.510G>T synonymous_variant 0.13
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyX 3067394 c.552G>T synonymous_variant 0.17
thyX 3067491 p.Ala152Val missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474982 p.Gly326Trp missense_variant 0.17
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiB 3642075 p.Asp181Asn missense_variant 0.13
fbiB 3642242 c.708C>A synonymous_variant 1.0
fbiB 3642306 p.Leu258Met missense_variant 0.2
alr 3841009 p.Leu138Phe missense_variant 0.13
rpoA 3878578 c.-71C>A upstream_gene_variant 0.67
rpoA 3878586 c.-79A>G upstream_gene_variant 0.67
rpoA 3878613 c.-113_-107delCAACCCA upstream_gene_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240192 c.330C>A synonymous_variant 0.14
embC 4240539 p.Pro226His missense_variant 0.2
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240877 p.Thr339Ala missense_variant 0.11
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243610 c.378G>T synonymous_variant 0.14
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244847 p.Gly539Cys missense_variant 0.22
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246389 p.Asp1053Asn missense_variant 0.14
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247871 p.Ala453Asp missense_variant 0.4
aftB 4268419 p.Glu140* stop_gained 0.12
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407835 p.Trp123* stop_gained 1.0
gid 4407873 c.330G>T synonymous_variant 1.0