TB-Profiler result

Run: SRR14088350
Summary

Run ID: SRR14088350

Sample name:

Date: 03-04-2023 09:45:13

Number of reads: 840518

Percentage reads mapped: 99.45

Strain: lineage3

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download PDF Download JSON
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
gyrA 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8837 c.1536C>A synonymous_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491502 p.Glu240Asp missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576540 p.Trp398Leu missense_variant 0.13
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761711 c.1905C>T synonymous_variant 0.12
rpoB 762274 p.Ala823Val missense_variant 0.15
rpoB 762310 p.His835Arg missense_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763468 c.99G>T synonymous_variant 0.13
rpoC 765688 c.2319G>T synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776009 c.2472A>G synonymous_variant 0.16
mmpL5 776018 c.2463G>C synonymous_variant 0.12
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777119 p.His454Gln missense_variant 0.15
mmpL5 777122 c.1359C>T synonymous_variant 0.15
mmpS5 778626 c.279_280insGTGAGCG frameshift_variant 0.14
mmpS5 778630 p.Leu92Phe missense_variant 0.13
mmpS5 778632 c.267_273delGCTCACC frameshift_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781763 c.204C>A synonymous_variant 0.12
fbiC 1304202 c.1272G>A synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473615 n.-43G>T upstream_gene_variant 0.14
rrl 1473780 n.123G>C non_coding_transcript_exon_variant 0.25
rrl 1475373 n.1716G>C non_coding_transcript_exon_variant 0.25
fabG1 1673495 p.Leu19Pro missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101762 c.1281C>A synonymous_variant 0.12
ndh 2102565 p.Arg160Trp missense_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156361 c.-250G>T upstream_gene_variant 0.12
PPE35 2167865 c.2748G>C synonymous_variant 0.21
PPE35 2167868 c.2745A>C synonymous_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167965 p.Ala883Gly missense_variant 0.17
PPE35 2167967 c.2646A>C synonymous_variant 0.17
PPE35 2169713 c.900C>G synonymous_variant 0.19
PPE35 2169717 p.Asn299Ile missense_variant 0.29
PPE35 2170048 p.Leu189Val missense_variant 0.55
PPE35 2170053 p.Thr187Ser missense_variant 0.6
PPE35 2170147 p.Ser156Ala missense_variant 0.14
PPE35 2170415 c.198A>G synonymous_variant 0.14
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
pncA 2290203 c.-962C>T upstream_gene_variant 0.14
kasA 2518407 p.Ala98Val missense_variant 0.14
kasA 2518864 c.750G>C synonymous_variant 0.12
kasA 2519140 c.1026G>C synonymous_variant 0.33
kasA 2519143 c.1029G>C synonymous_variant 0.29
eis 2715481 c.-149G>T upstream_gene_variant 0.2
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726269 p.Val26Gly missense_variant 0.24
folC 2746678 c.921T>C synonymous_variant 0.14
folC 2747630 c.-32G>A upstream_gene_variant 0.22
pepQ 2859548 p.Gly291Ser missense_variant 0.12
pepQ 2859737 p.Gly228Trp missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449049 c.546C>G synonymous_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474259 p.Gly85Ser missense_variant 0.14
Rv3236c 3612016 c.1101G>A synonymous_variant 0.18
Rv3236c 3612708 c.409T>C synonymous_variant 0.17
Rv3236c 3612838 c.279G>A synonymous_variant 0.12
Rv3236c 3612848 p.Leu90Pro missense_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.21
ddn 3986760 c.-84G>T upstream_gene_variant 0.22
clpC1 4039645 p.His354Asp missense_variant 0.17
clpC1 4040063 c.642G>T synonymous_variant 0.14
panD 4043909 p.Pro125Thr missense_variant 0.12
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242658 c.-575A>T upstream_gene_variant 0.13
embA 4244970 p.Leu580Met missense_variant 0.22
embA 4245700 p.Gly823Glu missense_variant 0.18
embB 4246133 c.-381G>A upstream_gene_variant 0.15
embB 4247473 c.960C>T synonymous_variant 0.11
embB 4249069 c.2556A>G synonymous_variant 0.11
embB 4249258 c.2745G>T synonymous_variant 1.0
aftB 4267583 c.1254C>T synonymous_variant 0.2
aftB 4267760 p.Asp359Glu missense_variant 0.22
whiB6 4338286 c.235delG frameshift_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408070 p.Trp45Arg missense_variant 1.0