TB-Profiler result

Run: SRR6650210
Summary

Run ID: SRR6650210

Sample name:

Date: 15-08-2023 08:20:50

Number of reads: 1700181

Percentage reads mapped: 99.28

Strain: lineage1.1.3.1

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
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.3 Indo-Oceanic EAI6 RD239 1.0
lineage1.1.3.1 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
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 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 490751 c.-32T>G upstream_gene_variant 0.21
fgd1 491008 p.Thr76Pro missense_variant 0.21
fgd1 491014 p.Thr78Pro missense_variant 0.42
fgd1 491027 p.Asn82Thr missense_variant 0.23
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619831 c.-60T>G upstream_gene_variant 0.16
ccsA 620545 p.Leu219Val missense_variant 0.18
ccsA 620551 p.Asp221His missense_variant 0.22
ccsA 620748 c.858T>G synonymous_variant 0.3
ccsA 620752 p.Arg288Gly missense_variant 0.28
ccsA 620756 p.Asp289Gly missense_variant 0.26
ccsA 620763 c.873G>A synonymous_variant 0.17
ccsA 620773 p.Ile295Val missense_variant 0.24
rpoB 759615 c.-192A>C upstream_gene_variant 0.21
rpoB 759620 c.-187A>C upstream_gene_variant 0.15
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 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779612 c.-707G>A upstream_gene_variant 1.0
rpsL 781363 c.-197T>G upstream_gene_variant 0.16
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801287 p.Val160Gly missense_variant 0.17
fbiC 1303016 p.Val29Gly missense_variant 0.22
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1461086 c.42A>G synonymous_variant 0.2
atpE 1461101 c.57T>G synonymous_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472505 n.660G>T non_coding_transcript_exon_variant 1.0
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.5
rrl 1474507 n.850G>C non_coding_transcript_exon_variant 0.33
fabG1 1673690 p.Val84Gly missense_variant 0.17
fabG1 1674076 p.Thr213Pro missense_variant 0.24
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918031 p.Lys31Arg missense_variant 0.17
tlyA 1918043 p.Asp35Ala missense_variant 0.21
tlyA 1918059 c.120C>A synonymous_variant 0.19
tlyA 1918664 p.Trp242* stop_gained 1.0
ndh 2102183 p.Arg287Thr missense_variant 1.0
ndh 2102499 p.Gly182Arg missense_variant 0.14
ndh 2102502 p.Thr181Pro missense_variant 0.15
ndh 2102517 p.Val176Phe missense_variant 0.21
ndh 2102520 p.Val175Leu missense_variant 0.22
ndh 2102524 c.519C>T synonymous_variant 0.18
ndh 2103225 c.-183A>C upstream_gene_variant 0.19
ndh 2103235 c.-193C>G upstream_gene_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167660 p.Thr985Pro missense_variant 0.18
PPE35 2167859 c.2754T>G synonymous_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168222 c.2391G>T synonymous_variant 1.0
PPE35 2170056 p.Val186Gly missense_variant 0.22
PPE35 2170066 p.Ala183Pro missense_variant 0.17
Rv1979c 2221818 c.1347T>C synonymous_variant 0.96
Rv1979c 2222075 p.Pro364Ser missense_variant 1.0
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 0.36
kasA 2518151 p.Ser13Arg missense_variant 0.19
eis 2714566 p.Leu256Pro missense_variant 0.15
eis 2715103 p.Leu77Pro missense_variant 0.22
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726267 c.75G>A synonymous_variant 0.28
ahpC 2726269 p.Val26Gly missense_variant 0.16
ahpC 2726277 p.Lys29Gln missense_variant 0.24
ahpC 2726286 p.Gly32Arg missense_variant 0.18
ahpC 2726338 p.Val49Gly missense_variant 0.28
ahpC 2726341 p.Val50Gly missense_variant 0.29
ahpC 2726345 c.153C>T synonymous_variant 0.25
ahpC 2726350 p.Trp53Leu missense_variant 0.24
pepQ 2859377 p.Thr348Ala missense_variant 0.17
pepQ 2859454 p.Val322Gly missense_variant 0.2
ribD 2987314 p.Leu159Pro missense_variant 0.2
ribD 2987316 p.Ala160Pro missense_variant 0.24
ribD 2987323 p.Val162Gly missense_variant 0.33
ribD 2987325 p.Ile163Val missense_variant 0.2
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyA 3074645 c.-174T>G upstream_gene_variant 0.18
thyA 3074648 c.-177T>G upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
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 0.96
whiB7 3568401 c.279G>C stop_lost&splice_region_variant 0.2
whiB7 3568417 p.Lys88Arg missense_variant 0.15
Rv3236c 3612388 c.729T>G synonymous_variant 0.19
Rv3236c 3612835 c.282T>G synonymous_variant 0.2
fbiB 3641583 p.Val17Ile missense_variant 1.0
alr 3841253 c.168C>T synonymous_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239973 c.111T>G synonymous_variant 0.19
embC 4240001 p.Thr47Pro missense_variant 0.22
embC 4240006 c.144A>C synonymous_variant 0.22
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242220 c.2358A>C synonymous_variant 0.29
embA 4242406 c.-827A>C upstream_gene_variant 0.16
embC 4242414 p.Leu851Arg missense_variant 0.18
embC 4242422 p.Trp854Gly missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243350 p.Thr40Pro missense_variant 0.22
embA 4243372 p.Gln47Arg missense_variant 0.17
embA 4243380 p.Thr50Pro missense_variant 0.19
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244638 p.Val469Gly missense_variant 0.23
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249323 p.Ala937Glu missense_variant 0.15
aftB 4268758 p.Ile27Val missense_variant 0.2
aftB 4268776 p.Ser21Gly missense_variant 0.33
aftB 4268786 c.51C>T synonymous_variant 0.16
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269486 c.-650T>G upstream_gene_variant 0.2
ubiA 4269502 p.Val111Gly missense_variant 0.31
aftB 4269504 c.-668A>G upstream_gene_variant 0.28
ubiA 4269511 p.Val108Gly missense_variant 0.22
ubiA 4269514 p.Val107Gly missense_variant 0.2
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326876 p.Lys200Gln missense_variant 0.14
ethR 4327813 p.Thr89Pro missense_variant 0.17
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 1.0