TB-Profiler result

Run: SRR6650428
Summary

Run ID: SRR6650428

Sample name:

Date: 15-08-2023 07:39:45

Number of reads: 604298

Percentage reads mapped: 99.31

Strain: lineage1.2.2.2

Drug-resistance: Sensitive

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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
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 0.99
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
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 5530 c.291C>T synonymous_variant 1.0
gyrB 6112 p.Met291Ile missense_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 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620586 c.696C>T synonymous_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.31
ccsA 620752 p.Arg288Gly missense_variant 0.21
ccsA 620756 p.Asp289Gly missense_variant 0.5
ccsA 620763 c.873G>A synonymous_variant 0.29
ccsA 620770 p.Trp294Arg missense_variant 0.2
ccsA 620773 p.Ile295Val missense_variant 0.19
ccsA 620778 p.Asn296Lys missense_variant 0.14
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
rpoC 765889 c.2520C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777155 c.1326G>C synonymous_variant 1.0
mmpL5 778239 p.Val81Gly missense_variant 0.33
mmpR5 779363 p.Leu125Arg missense_variant 0.14
rpsL 781363 c.-197T>G upstream_gene_variant 0.3
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302948 c.18T>G synonymous_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673690 p.Val84Gly missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102538 p.Lys169Gln missense_variant 0.25
ndh 2102540 p.Ala168Gly missense_variant 0.29
ndh 2103225 c.-183A>C upstream_gene_variant 0.2
ndh 2103227 c.-185T>C upstream_gene_variant 0.33
ndh 2103235 c.-193C>G upstream_gene_variant 0.44
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2170082 c.531T>G synonymous_variant 0.2
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288951 c.291T>G synonymous_variant 0.2
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.4
kasA 2518151 p.Ser13Arg missense_variant 0.33
kasA 2518161 p.Val16Gly missense_variant 0.2
eis 2715103 p.Leu77Pro missense_variant 0.25
eis 2715396 c.-64G>T upstream_gene_variant 0.15
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726265 p.Lys25Gln missense_variant 0.23
ahpC 2726286 p.Gly32Arg missense_variant 0.14
ahpC 2726338 p.Val49Gly missense_variant 0.2
ahpC 2726341 p.Val50Gly missense_variant 0.2
ahpC 2726345 c.153C>T synonymous_variant 0.2
ahpC 2726350 p.Trp53Leu missense_variant 0.2
ahpC 2726355 p.Lys55Glu missense_variant 0.22
folC 2746745 p.Val285Gly missense_variant 0.18
folC 2746832 p.Val256Gly missense_variant 0.29
pepQ 2859377 p.Thr348Ala missense_variant 0.18
pepQ 2859438 c.981T>G synonymous_variant 0.33
pepQ 2859904 p.Val172Gly missense_variant 0.33
ribD 2987307 p.Ala157Pro missense_variant 0.25
ribD 2987316 p.Ala160Pro missense_variant 0.33
ribD 2987323 p.Val162Gly missense_variant 0.44
ribD 2987331 p.Cys165Gly missense_variant 0.33
ribD 2987337 p.Gly167Arg missense_variant 0.22
Rv2752c 3064889 p.Lys435Glu missense_variant 1.0
Rv2752c 3066103 p.Asn30Ser missense_variant 1.0
thyA 3074608 c.-137A>G upstream_gene_variant 0.2
thyA 3074628 c.-157G>C upstream_gene_variant 0.17
thyA 3074633 c.-162C>G upstream_gene_variant 0.17
thyA 3074641 c.-170C>T upstream_gene_variant 0.4
thyA 3074645 c.-174T>G upstream_gene_variant 0.38
thyA 3074648 c.-177T>G upstream_gene_variant 0.44
thyA 3074654 c.-183T>G upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.53
fbiD 3339279 c.162T>G synonymous_variant 0.33
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
whiB7 3568417 p.Lys88Arg missense_variant 0.33
whiB7 3568425 c.255T>C synonymous_variant 0.4
Rv3236c 3612419 p.Ala233Gly missense_variant 0.15
Rv3236c 3612800 p.Val106Gly missense_variant 0.23
Rv3236c 3612835 c.282T>G synonymous_variant 0.33
alr 3841546 c.-126C>A upstream_gene_variant 1.0
clpC1 4039484 c.1221T>G synonymous_variant 0.2
clpC1 4040447 c.257delA frameshift_variant 0.17
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239973 c.111T>G synonymous_variant 0.42
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242220 c.2358A>C synonymous_variant 0.33
embC 4242414 p.Leu851Arg missense_variant 0.22
embC 4242422 p.Trp854Gly missense_variant 0.3
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244641 p.Val470Gly missense_variant 0.29
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247577 p.Leu355Arg missense_variant 0.2
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249298 p.Trp929Gly missense_variant 0.17
embB 4249305 p.Asn931Thr missense_variant 0.25
embB 4249316 p.Ala935Pro missense_variant 0.2
embB 4249322 p.Ala937Lys missense_variant 0.3
aftB 4268776 p.Ser21Gly missense_variant 0.22
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethR 4327768 p.Thr74Pro missense_variant 0.2
ethR 4327813 p.Thr89Pro missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
whiB6 4338635 c.-114A>C upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0