TB-Profiler result

Run: ERR775802
Summary

Run ID: ERR775802

Sample name:

Date: 02-04-2023 05:43:01

Number of reads: 767087

Percentage reads mapped: 98.83

Strain: lineage1.1.1

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 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.1 Indo-Oceanic EAI4;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 761139 p.His445Tyr missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674481 p.Ser94Ala missense_variant 1.0 isoniazid, 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 6112 p.Met291Ile missense_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 1.0
mshA 575491 c.144G>T synonymous_variant 0.12
rpoB 760386 p.His194Tyr missense_variant 1.0
rpoB 761476 p.Arg557His missense_variant 1.0
rpoB 762732 p.Glu976Lys missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763158 c.-212C>T upstream_gene_variant 0.14
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776422 p.Asp687Tyr missense_variant 0.15
mmpL5 776478 p.Ala668Val missense_variant 0.12
mmpL5 778116 p.His122Arg missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474084 n.427G>T non_coding_transcript_exon_variant 0.18
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 1.0
rrl 1475513 n.1856T>C non_coding_transcript_exon_variant 0.25
rpsA 1834319 p.Val260Ile missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169398 c.1215C>A synonymous_variant 0.17
PPE35 2170460 c.153G>A synonymous_variant 0.13
Rv1979c 2222083 p.Leu361Pro missense_variant 0.33
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726070 c.-123G>A upstream_gene_variant 1.0
folC 2747002 c.597T>C synonymous_variant 0.12
folC 2747033 p.Ala189Glu missense_variant 0.12
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087507 p.Lys230Glu missense_variant 0.17
fbiD 3339273 c.156T>G synonymous_variant 0.32
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449677 p.Asn392Asp missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475302 c.1296C>T synonymous_variant 1.0
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4039484 c.1221T>G synonymous_variant 0.33
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244096 c.864C>T synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269152 p.Ala228Ser missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4327483 c.-10G>A upstream_gene_variant 1.0
whiB6 4338242 p.Gln94Glu missense_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 4407791 p.Ala138Thr missense_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0