TB-Profiler result

Run: ERR117618
Summary

Run ID: ERR117618

Sample name:

Date: 31-03-2023 12:14:03

Number of reads: 5594603

Percentage reads mapped: 99.28

Strain: lineage1.1.1

Drug-resistance: Pre-XDR-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 0.97
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.98
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.94
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
gyrA 7582 p.Asp94Gly missense_variant 0.97 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.94 rifampicin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.92 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.97 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.94 isoniazid
pncA 2288946 c.295delT frameshift_variant 0.98 pyrazinamide
alr 3840393 p.Met343Thr missense_variant 0.96 cycloserine
embB 4247431 p.Met306Ile missense_variant 0.95 ethambutol
gid 4408100 c.102delG frameshift_variant 0.97 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 0.94
gyrA 6439 c.-863C>G upstream_gene_variant 0.97
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.99
gyrA 7853 c.552C>T synonymous_variant 0.96
gyrA 8452 p.Ala384Val missense_variant 0.96
gyrA 9143 c.1842T>C synonymous_variant 0.95
gyrA 9304 p.Gly668Asp missense_variant 0.96
fgd1 491742 c.960T>C synonymous_variant 0.96
rpoC 763031 c.-339T>C upstream_gene_variant 0.94
rpoC 763884 p.Ala172Val missense_variant 0.99
rpoC 763886 c.517C>A synonymous_variant 0.98
rpoC 765171 p.Pro601Leu missense_variant 0.97
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.95
rpsL 781395 c.-165T>C upstream_gene_variant 0.98
rpsL 781821 p.Lys88Glu missense_variant 0.97
embR 1417019 p.Cys110Tyr missense_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834184 p.Val215Ile missense_variant 0.96
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101976 p.Pro356Leu missense_variant 0.94
katG 2154724 p.Arg463Leu missense_variant 0.98
PPE35 2167926 p.Leu896Ser missense_variant 0.96
PPE35 2167983 p.Gly877Asp missense_variant 0.98
PPE35 2169829 p.Ala262Thr missense_variant 0.97
Rv1979c 2222308 p.Asp286Gly missense_variant 0.99
Rv1979c 2223124 p.Leu14Arg missense_variant 0.97
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289517 c.-276C>G upstream_gene_variant 0.93
kasA 2518132 c.18C>T synonymous_variant 0.96
ahpC 2726051 c.-142G>A upstream_gene_variant 0.97
Rv2752c 3064632 c.1560C>T synonymous_variant 0.98
thyA 3074495 c.-24C>T upstream_gene_variant 0.97
ald 3086788 c.-32T>C upstream_gene_variant 0.98
ald 3087660 c.843dupC frameshift_variant 0.96
Rv3083 3448714 p.Asp71His missense_variant 0.98
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
fprA 3474342 c.336G>A synonymous_variant 0.98
fprA 3474597 c.591C>A synonymous_variant 0.99
fprA 3475159 p.Asn385Asp missense_variant 0.98
fbiB 3641951 c.417G>T synonymous_variant 0.95
rpoA 3878075 p.Gly145Cys missense_variant 0.36
clpC1 4040517 p.Val63Ala missense_variant 0.98
embC 4240671 p.Thr270Ile missense_variant 0.96
embC 4241042 p.Asn394Asp missense_variant 0.96
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.94
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 0.95
ubiA 4269387 p.Glu149Asp missense_variant 0.96
aftB 4269606 c.-770T>C upstream_gene_variant 0.99
ethA 4326134 p.Pro447Arg missense_variant 0.94
ethA 4326290 p.Ala395Val missense_variant 0.95
ethA 4326398 p.Gln359Arg missense_variant 0.95
whiB6 4338242 p.Gln94Glu missense_variant 0.94
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.99
gid 4407588 c.615A>G synonymous_variant 0.98
gid 4407873 c.330G>T synonymous_variant 0.97