TB-Profiler result

Run: SRR6650111
Summary

Run ID: SRR6650111

Sample name:

Date: 15-08-2023 07:56:18

Number of reads: 884904

Percentage reads mapped: 99.32

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 0.99
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 5440 c.201A>C synonymous_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6918 p.His560Leu missense_variant 0.22
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 8423 c.1122G>A synonymous_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 490979 p.Asn66Thr missense_variant 0.18
fgd1 491014 p.Thr78Pro missense_variant 0.24
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576698 p.Glu451Gln missense_variant 0.15
mshA 576723 p.Val459Gly missense_variant 0.18
ccsA 619831 c.-60T>G upstream_gene_variant 0.33
ccsA 619835 c.-56G>T upstream_gene_variant 0.22
ccsA 619844 c.-47T>G upstream_gene_variant 0.3
ccsA 620532 c.642T>G synonymous_variant 0.18
ccsA 620752 p.Arg288Gly missense_variant 0.2
ccsA 620756 p.Asp289Gly missense_variant 0.27
ccsA 620778 p.Asn296Lys missense_variant 0.17
rpoB 759611 c.-196G>C upstream_gene_variant 0.21
rpoB 759615 c.-192A>C upstream_gene_variant 0.21
rpoB 759620 c.-187A>C upstream_gene_variant 0.23
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 764086 c.717C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778282 p.Asp67His missense_variant 0.23
rpsL 781363 c.-197T>G upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781524 c.-36C>A upstream_gene_variant 0.15
rplC 800963 p.Leu52Arg missense_variant 0.19
rplC 801287 p.Val160Gly missense_variant 0.19
fbiC 1302890 c.-41G>T upstream_gene_variant 1.0
fbiC 1304125 p.Val399Leu missense_variant 0.18
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472115 n.270C>T non_coding_transcript_exon_variant 1.0
rrl 1473927 n.270C>G non_coding_transcript_exon_variant 0.33
rrl 1473932 n.275C>A non_coding_transcript_exon_variant 0.33
rrl 1473953 n.296T>G non_coding_transcript_exon_variant 0.38
rrl 1473959 n.302T>G non_coding_transcript_exon_variant 0.38
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.5
rrl 1474500 n.843T>G non_coding_transcript_exon_variant 0.8
rrl 1476176 n.2519C>G non_coding_transcript_exon_variant 0.18
rrl 1476274 n.2617G>A non_coding_transcript_exon_variant 0.2
rrl 1476313 n.2656G>T non_coding_transcript_exon_variant 1.0
rrl 1476585 n.2928A>C non_coding_transcript_exon_variant 0.2
fabG1 1674076 p.Thr213Pro missense_variant 0.27
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918059 c.120C>A synonymous_variant 0.25
tlyA 1918065 c.126G>C synonymous_variant 0.22
ndh 2102144 p.Ala300Val missense_variant 0.14
ndh 2102498 p.Gly182Val missense_variant 0.15
ndh 2103225 c.-183A>C upstream_gene_variant 0.47
ndh 2103227 c.-185T>C upstream_gene_variant 0.2
ndh 2103231 c.-189G>T upstream_gene_variant 0.19
ndh 2103235 c.-193C>G upstream_gene_variant 0.29
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167941 p.Ser891Asn missense_variant 0.29
PPE35 2168028 p.Pro862His missense_variant 0.17
PPE35 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2169299 p.Asn438Lys missense_variant 0.29
PPE35 2169320 p.Leu431Phe missense_variant 0.14
Rv1979c 2221919 p.Val416Met missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289500 c.-259A>G upstream_gene_variant 0.18
pncA 2289511 c.-270T>G upstream_gene_variant 0.18
pncA 2290087 c.-846T>G upstream_gene_variant 0.15
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.33
kasA 2518151 p.Ser13Arg missense_variant 0.27
eis 2714753 p.Gln194* stop_gained 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746745 p.Val285Gly missense_variant 0.5
pepQ 2859400 p.Asp340Gly missense_variant 0.2
pepQ 2859438 c.981T>G synonymous_variant 0.38
ribD 2986908 p.Thr24Pro missense_variant 0.15
ribD 2987316 p.Ala160Pro missense_variant 0.24
ribD 2987320 p.Glu161Gly missense_variant 0.19
ribD 2987323 p.Val162Gly missense_variant 0.44
ribD 2987337 p.Gly167Arg missense_variant 0.19
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.28
fbiD 3339608 p.Pro164Arg missense_variant 0.21
fbiD 3339626 p.His170Pro missense_variant 0.2
Rv3083 3448714 p.Asp71His missense_variant 0.91
Rv3083 3448745 p.Ile81Thr missense_variant 0.2
Rv3083 3448757 p.Ile85Thr missense_variant 0.27
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 3612557 p.Val187Gly missense_variant 0.33
Rv3236c 3612835 c.282T>G synonymous_variant 0.18
fbiB 3642095 c.561G>A synonymous_variant 0.13
fbiB 3642759 p.Arg409Gly missense_variant 0.2
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239973 c.111T>G synonymous_variant 0.24
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242220 c.2358A>C synonymous_variant 0.22
embA 4242406 c.-827A>C upstream_gene_variant 0.24
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244621 p.Leu463Phe missense_variant 0.12
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249738 c.3225C>A synonymous_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269504 c.-668A>G upstream_gene_variant 0.27
ubiA 4269511 p.Val108Gly missense_variant 0.36
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269859 c.-26A>C upstream_gene_variant 0.19
ethA 4326148 c.1326G>T synonymous_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethR 4326898 c.-651C>G upstream_gene_variant 0.21
ethA 4326905 p.Leu190Pro missense_variant 0.21
ethR 4327813 p.Thr89Pro missense_variant 0.17
ethR 4327819 p.Ala91Pro missense_variant 0.17
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
gid 4407921 c.282A>G synonymous_variant 0.13