TB-Profiler result

Run: SRR6930923

Summary

Run ID: SRR6930923

Sample name:

Date: 04-04-2023 18:13:27

Number of reads: 1590656

Percentage reads mapped: 99.38

Strain: lineage1.2.2.2

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 1.0
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.2 Indo-Oceanic NA 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
gyrA 7563 p.Gly88Cys missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 760314 p.Val170Phe missense_variant 1.0 rifampicin
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide
embB 4247429 p.Met306Leu missense_variant 0.99 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 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7268 c.-34C>T upstream_gene_variant 0.99
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
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 765909 p.Leu847Arg missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile 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
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.99
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2170516 p.Gly33Arg missense_variant 1.0
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
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339390 c.273A>G synonymous_variant 0.98
Rv3083 3448714 p.Asp71His missense_variant 0.98
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
whiB7 3568425 c.255T>G synonymous_variant 1.0
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 4243294 p.Gly21Glu missense_variant 1.0
embA 4245098 c.1866C>T synonymous_variant 0.99
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247360 p.Val283Met missense_variant 0.97
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326148 c.1326G>T synonymous_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 0.99
ethA 4327707 c.-234G>C upstream_gene_variant 1.0
whiB6 4338203 p.Arg107Cys missense_variant 0.97
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 4407873 c.330G>T synonymous_variant 1.0
gid 4407902 p.Leu101Phe missense_variant 1.0
gid 4407948 p.Asp85Glu missense_variant 1.0