TB-Profiler result

Run: ERR4816576
Summary

Run ID: ERR4816576

Sample name:

Date: 01-04-2023 14:30:31

Number of reads: 935110

Percentage reads mapped: 99.3

Strain: lineage1.1.2

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674263 p.Ile21Thr missense_variant 1.0 isoniazid, ethionamide
katG 2155740 c.371delG frameshift_variant 0.17 isoniazid, isoniazid
gid 4407851 c.351dupG frameshift_variant 1.0 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 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrB 6363 c.1127delG frameshift_variant 0.11
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 9047 c.1746C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9194 c.1893G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9443 c.2142G>A synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576000 p.Asp218Ala missense_variant 1.0
ccsA 620594 p.Phe235Ser missense_variant 0.11
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoB 761104 p.Phe433Ser missense_variant 0.11
rpoB 761823 p.Asn673Asp missense_variant 0.12
rpoC 762698 c.-672C>T upstream_gene_variant 0.22
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 763998 p.Asp210Gly missense_variant 0.13
rpoC 764449 c.1080G>T synonymous_variant 0.12
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 766265 p.Leu966Val missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 1.0
mmpL5 777265 p.Leu406Met missense_variant 0.11
mmpR5 779478 p.Glu163Asp missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416510 p.Arg280Cys missense_variant 0.14
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472967 n.1122G>A non_coding_transcript_exon_variant 0.5
rrl 1476638 n.2981C>A non_coding_transcript_exon_variant 1.0
fabG1 1673895 p.Asn152Lys missense_variant 0.25
inhA 1674069 c.-133G>A upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103193 c.-151G>A upstream_gene_variant 0.2
katG 2154322 p.Tyr597Cys missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155146 c.966G>T synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168900 c.1713G>A synonymous_variant 0.12
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289471 c.-230C>A upstream_gene_variant 0.17
kasA 2517997 c.-118A>G upstream_gene_variant 0.17
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518600 c.490delG frameshift_variant 0.12
kasA 2518677 p.Gly188Ala missense_variant 0.14
kasA 2518849 c.735G>T synonymous_variant 0.12
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
pepQ 2860138 p.Lys94Arg missense_variant 0.11
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065305 p.Ala296Val missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087094 p.Phe92Tyr missense_variant 0.11
fbiD 3339703 p.Thr196Ser missense_variant 0.14
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448944 c.441G>T synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474849 p.Lys281Asn missense_variant 0.17
fprA 3474946 p.Pro314Ser missense_variant 0.17
fprA 3474981 c.979delG frameshift_variant 0.25
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612461 p.Leu219Ser missense_variant 0.11
alr 3840237 p.Arg395Leu missense_variant 0.12
ddn 3986942 c.103delG frameshift_variant 0.17
ddn 3987057 p.Arg72Trp missense_variant 0.97
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4044420 c.-139G>A upstream_gene_variant 0.12
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242161 p.Ala767Thr missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249764 p.Thr1084Asn missense_variant 0.25
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4327351 p.Met41Ile missense_variant 0.18
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 0.95
gid 4407873 c.330G>T synonymous_variant 1.0