TB-Profiler result

Run: ERR245747
Summary

Run ID: ERR245747

Sample name:

Date: 31-03-2023 18:18:36

Number of reads: 5653710

Percentage reads mapped: 98.93

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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 761095 p.Leu430Pro missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9596 c.2295G>T synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620407 p.Pro173Ala missense_variant 0.3
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 762249 p.Leu815Val missense_variant 0.22
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.26
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764181 p.Asp271Gly missense_variant 1.0
rpoC 765734 p.Leu789Ala missense_variant 1.0
rpoC 767305 p.Tyr1312* stop_gained 0.22
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
rplC 800997 p.Asn63Lys missense_variant 0.19
embR 1417501 c.-154A>C upstream_gene_variant 0.27
atpE 1461019 c.-26C>A upstream_gene_variant 0.24
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.26
inhA 1674892 p.Asn231Asp missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167871 c.2742G>C synonymous_variant 0.24
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169866 c.747G>C synonymous_variant 0.32
PPE35 2170769 c.-157C>T upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518144 c.29dupG frameshift_variant 0.11
eis 2714366 p.Val323Leu missense_variant 0.26
eis 2715586 c.-254G>C upstream_gene_variant 0.45
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
ribD 2987307 p.Ala157Pro missense_variant 0.17
thyA 3073806 c.666C>G synonymous_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641271 p.Tyr243* stop_gained 0.29
fbiB 3641955 p.Gly141Arg missense_variant 0.22
fbiB 3642734 c.1200G>C synonymous_variant 0.26
clpC1 4038857 c.1848C>A synonymous_variant 0.19
clpC1 4039932 p.Gly258Val missense_variant 0.28
embC 4241429 p.Phe523Val missense_variant 0.43
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242425 p.Arg855Gly missense_variant 0.21
embC 4242476 p.Pro872Ala missense_variant 0.27
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.3
embA 4243190 c.-43G>C upstream_gene_variant 1.0
embA 4244375 c.1143C>G synonymous_variant 0.35
embB 4247041 c.528C>T synonymous_variant 0.23
ubiA 4269529 p.Ala102Gly missense_variant 0.19
ethA 4327672 c.-199G>A upstream_gene_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0