TB-Profiler result

Run: SRR6650385
Summary

Run ID: SRR6650385

Sample name:

Date: 15-08-2023 07:38:49

Number of reads: 529026

Percentage reads mapped: 99.33

Strain: lineage1.2.2.2

Drug-resistance: Other

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol R embB p.Asp354Ala (0.22)
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
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 0.99
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
embB 4247574 p.Asp354Ala missense_variant 0.22 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
gyrB 6182 p.Thr315Ala 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 8674 p.Ile458Thr missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9585 p.Leu762Val missense_variant 0.33
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576723 p.Val459Gly missense_variant 0.36
ccsA 620551 p.Asp221His missense_variant 0.22
ccsA 620748 c.858T>G synonymous_variant 0.42
ccsA 620752 p.Arg288Gly missense_variant 0.5
ccsA 620756 p.Asp289Gly missense_variant 0.58
ccsA 620761 p.Lys291Gln missense_variant 0.17
ccsA 620765 p.Ala292Gly missense_variant 0.18
ccsA 620770 p.Trp294Arg missense_variant 0.27
ccsA 620773 p.Ile295Val missense_variant 0.64
ccsA 620779 p.Val297Phe missense_variant 0.18
ccsA 620788 p.Phe300Leu missense_variant 0.18
ccsA 620801 p.Val304Gly missense_variant 0.18
rpoB 760703 c.897C>T synonymous_variant 1.0
rpoB 761725 p.Glu640Gly missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778270 p.Ser71Ala missense_variant 0.25
mmpL5 778282 p.Asp67His missense_variant 0.18
mmpR5 779348 p.Val120Gly missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801287 p.Val160Gly missense_variant 0.6
fbiC 1303016 p.Val29Gly missense_variant 0.33
Rv1258c 1406452 p.Thr297Pro missense_variant 0.17
Rv1258c 1407081 p.Ala87Gly missense_variant 0.33
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476219 n.2562T>G non_coding_transcript_exon_variant 0.17
fabG1 1674076 p.Thr213Pro missense_variant 0.18
rpsA 1834666 c.1125G>A synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918010 p.Ala24Gly missense_variant 0.22
tlyA 1918029 c.90C>A synonymous_variant 0.22
tlyA 1918055 p.Ala39Gly missense_variant 0.25
tlyA 1918059 c.120C>A synonymous_variant 0.38
ndh 2103225 c.-183A>C upstream_gene_variant 0.88
ndh 2103227 c.-185T>C upstream_gene_variant 0.5
ndh 2103229 c.-187C>A upstream_gene_variant 0.25
ndh 2103235 c.-193C>G upstream_gene_variant 0.86
ndh 2103239 c.-197T>G upstream_gene_variant 0.38
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167660 p.Thr985Pro missense_variant 0.33
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2168885 c.1728A>C synonymous_variant 1.0
PPE35 2169293 c.1320T>G synonymous_variant 0.2
PPE35 2170056 p.Val186Gly missense_variant 0.18
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.25
kasA 2518151 p.Ser13Arg missense_variant 0.27
eis 2714569 p.Ala255Gly missense_variant 0.2
eis 2714670 p.Asp221Glu missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ribD 2987323 p.Val162Gly missense_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087909 p.Thr364Pro missense_variant 0.38
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448813 p.Val104Phe missense_variant 0.25
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
whiB7 3568417 p.Lys88Arg missense_variant 0.15
whiB7 3568419 c.261C>A synonymous_variant 0.15
Rv3236c 3612776 p.Asp114Gly missense_variant 0.22
Rv3236c 3612780 p.Leu113Val missense_variant 0.22
Rv3236c 3612784 p.Leu111Phe missense_variant 0.22
Rv3236c 3612789 p.Leu110Val missense_variant 0.22
Rv3236c 3612797 p.Ala107Gly missense_variant 0.22
Rv3236c 3612800 p.Val106Gly missense_variant 0.22
Rv3236c 3612835 c.282T>G synonymous_variant 0.5
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239973 c.111T>G synonymous_variant 0.17
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242220 c.2358A>C synonymous_variant 0.25
embA 4242406 c.-827A>C upstream_gene_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243350 p.Thr40Pro missense_variant 0.18
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247577 p.Leu355Arg missense_variant 0.22
embB 4247590 c.1077A>G synonymous_variant 0.17
embB 4247599 p.Trp362Cys missense_variant 0.2
embB 4247607 p.Leu365Arg missense_variant 0.18
embB 4247614 c.1101T>G synonymous_variant 0.2
embB 4247616 p.Glu368Gly missense_variant 0.2
embB 4247619 p.Val369Gly missense_variant 0.2
embB 4247623 c.1110G>C synonymous_variant 0.3
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249403 p.Thr964Pro missense_variant 0.5
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269504 c.-668A>G upstream_gene_variant 0.2
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 4326887 p.Asp196Gly missense_variant 0.33
ethR 4327639 p.Ala31Pro missense_variant 0.2
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 4407873 c.330G>T synonymous_variant 1.0