TB-Profiler result

Run: SRR6207291
Summary

Run ID: SRR6207291

Sample name:

Date: 02-08-2023 15:14:55

Number of reads: NA

Percentage reads mapped: NA

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 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761140 p.His445Leu missense_variant 1.0 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.88 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288852 c.375_389delCGATGAGGTCGATGT disruptive_inframe_deletion 1.0 pyrazinamide
embA 4243203 c.-29_-28delCT upstream_gene_variant 1.0 ethambutol
embB 4247445 p.Asp311Gly missense_variant 0.22 ethambutol
embB 4248003 p.Gln497Arg 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
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 1.0
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 8935 p.Gln545Leu missense_variant 0.17
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9752 c.2451C>A synonymous_variant 0.12
fgd1 491012 p.Pro77His missense_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575750 p.Gly135Trp missense_variant 0.15
mshA 576425 p.Val360Met missense_variant 0.11
mshA 576611 p.Ala422Pro missense_variant 0.67
rpoB 760139 c.333A>G synonymous_variant 0.17
rpoB 762322 p.Gly839Val missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763552 c.183C>T synonymous_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 766493 p.Gly1042Cys missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776741 c.1740C>G synonymous_variant 0.11
mmpL5 777741 c.736_739delGGCG frameshift_variant 0.12
mmpL5 777753 c.727delA frameshift_variant 0.13
mmpL5 777773 c.708G>T synonymous_variant 0.12
mmpR5 778295 c.-695C>T upstream_gene_variant 0.18
mmpS5 779625 c.-720G>A upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406671 p.Val224Leu missense_variant 0.13
embR 1416797 p.Cys184Phe missense_variant 0.17
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474863 n.1206A>G non_coding_transcript_exon_variant 0.15
fabG1 1673608 p.Gly57Arg missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102240 p.Arg268His missense_variant 1.0
ndh 2102486 p.Ala186Val missense_variant 0.12
katG 2154006 c.2106G>C synonymous_variant 0.12
katG 2154252 c.1860T>C synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155495 p.Gly206Asp missense_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.29
PPE35 2170053 p.Thr187Ser missense_variant 0.25
Rv1979c 2222098 p.Thr356Lys missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289169 p.Ala25Thr missense_variant 0.14
pncA 2289424 c.-183C>A upstream_gene_variant 0.12
pncA 2290065 c.-824G>T upstream_gene_variant 0.2
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518515 p.Pro134His missense_variant 0.18
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
pepQ 2859382 p.Gly346Asp missense_variant 0.14
ribD 2987128 p.Arg97Gln missense_variant 0.13
thyX 3068062 c.-117A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087837 p.Ala340Thr missense_variant 0.15
Rv3083 3448558 p.Thr19Ser missense_variant 0.15
Rv3083 3448714 p.Asp71His missense_variant 1.0
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
Rv3236c 3612467 p.Gln217Arg missense_variant 0.14
Rv3236c 3612749 p.Gly123Val missense_variant 0.12
fbiB 3640588 c.-947C>T upstream_gene_variant 0.15
fbiA 3641101 c.561_563delTGT disruptive_inframe_deletion 0.13
fbiB 3641583 p.Val17Phe missense_variant 0.12
fbiB 3642194 c.660C>T synonymous_variant 0.14
fbiB 3642772 p.Asp413Ala missense_variant 0.25
fbiB 3642867 p.Leu445Met missense_variant 0.13
clpC1 4039308 p.Lys466Arg missense_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040719 c.-15A>G upstream_gene_variant 1.0
embC 4240280 p.Val140Phe missense_variant 0.12
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242133 c.2271G>T synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245670 p.Ala813Gly missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.17
embB 4246555 c.42G>C synonymous_variant 0.17
embB 4246556 p.Ala15Pro missense_variant 0.17
embB 4246979 p.Gly156Cys missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249610 p.Asn1033Asp missense_variant 0.14
aftB 4267853 c.984G>A synonymous_variant 0.12
aftB 4267960 p.Val293Met 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 1.0
ethA 4327827 c.-354A>G upstream_gene_variant 0.27
whiB6 4338203 p.Arg107Cys missense_variant 1.0
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 4407848 p.Ala119Thr missense_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0