TB-Profiler result

Run: SRR22424879
Summary

Run ID: SRR22424879

Sample name:

Date: 04-04-2023 04:15:10

Number of reads: 1148291

Percentage reads mapped: 99.59

Strain: lineage3.1.2.1

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 1.0
lineage3.1.2.1 East-African-Indian CAS2 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 7581 p.Asp94Tyr missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288805 p.Ala146Glu missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764346 p.Pro326Leu missense_variant 0.11
rpoC 764724 p.Phe452Cys missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777590 c.891G>T synonymous_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800757 c.-52G>T upstream_gene_variant 0.17
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476750 n.3093T>A non_coding_transcript_exon_variant 0.13
inhA 1673431 c.-771G>A upstream_gene_variant 1.0
inhA 1674858 p.Glu219Asp missense_variant 0.11
rpsA 1834660 c.1119C>T synonymous_variant 0.13
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
PPE35 2168604 p.Pro670Leu missense_variant 1.0
PPE35 2168775 p.Pro613Leu missense_variant 0.2
PPE35 2170053 p.Thr187Ser missense_variant 0.13
PPE35 2170471 p.Val48Leu missense_variant 0.12
Rv1979c 2223097 p.Gly23Val missense_variant 0.12
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 2518506 c.395delG frameshift_variant 0.1
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2747731 c.-133C>T upstream_gene_variant 0.17
pepQ 2859715 p.Arg235His missense_variant 0.13
Rv2752c 3064535 p.Pro553Thr missense_variant 0.11
thyX 3067949 c.-4C>A upstream_gene_variant 1.0
thyA 3074182 p.Gln97Arg missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339304 c.192delC frameshift_variant 0.17
fbiD 3339554 p.Thr146Ile missense_variant 0.11
Rv3083 3448505 c.2T>C start_lost 0.1
fprA 3473822 c.-185C>T upstream_gene_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612006 p.Arg371Cys missense_variant 0.11
Rv3236c 3612087 p.Ala344Ser missense_variant 0.18
rpoA 3878275 p.Leu78Pro missense_variant 0.12
clpC1 4040332 p.Val125Phe missense_variant 0.14
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243639 p.Cys136Phe missense_variant 0.11
embB 4249059 p.Thr849Asn missense_variant 0.12
aftB 4267636 c.1201C>A synonymous_variant 0.13
aftB 4268050 c.786delG frameshift_variant 0.15
ubiA 4269721 p.Ala38Val missense_variant 1.0
ethR 4326676 c.-873G>A upstream_gene_variant 0.12
ethA 4327058 p.Gly139Ala missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 0.93
gid 4407588 c.615A>G synonymous_variant 1.0