TB-Profiler result

Run: SRR6964552
Summary

Run ID: SRR6964552

Sample name:

Date: 04-04-2023 18:16:50

Number of reads: 3852091

Percentage reads mapped: 99.33

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 0.92
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 0.36 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpsL 781687 p.Lys43Arg missense_variant 0.1 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.17 isoniazid
gid 4408025 p.Glu60* stop_gained 0.47 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 0.18
gyrB 6124 c.885C>T synonymous_variant 0.19
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8948 c.1647G>A synonymous_variant 0.61
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 0.87
rpoB 761231 c.1425C>T synonymous_variant 0.44
rpoC 762434 c.-936T>G upstream_gene_variant 0.91
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.12
rpoC 763886 c.517C>A synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777323 c.1158C>T synonymous_variant 0.11
mmpL5 777647 c.834C>T synonymous_variant 0.49
rpsL 781395 c.-165T>C upstream_gene_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 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.54
pncA 2289365 c.-125delC upstream_gene_variant 0.91
ahpC 2726105 c.-88G>A upstream_gene_variant 0.96
pepQ 2859841 p.Ile193Thr missense_variant 0.42
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474901 p.Ser299Arg missense_variant 0.52
fprA 3474993 c.987G>A synonymous_variant 0.5
fprA 3475159 p.Asn385Asp missense_variant 0.17
fbiB 3642877 p.Lys448Arg missense_variant 0.29
embC 4240671 p.Thr270Ile missense_variant 0.11
embC 4241042 p.Asn394Asp missense_variant 0.11
embC 4242075 p.Arg738Gln missense_variant 0.85
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 0.12
embB 4249000 c.2487T>G synonymous_variant 0.61
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.15
gid 4407588 c.615A>G synonymous_variant 1.0