TB-Profiler result

Run: SRR6650227
Summary

Run ID: SRR6650227

Sample name:

Date: 15-08-2023 08:20:58

Number of reads: 1355056

Percentage reads mapped: 99.27

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 0.99
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
gyrB 6298 c.1059C>T synonymous_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 490979 p.Asn66Thr missense_variant 0.2
fgd1 491008 p.Thr76Pro missense_variant 0.24
fgd1 491014 p.Thr78Pro missense_variant 0.4
fgd1 491018 p.Phe79Ser missense_variant 0.22
fgd1 491027 p.Asn82Thr missense_variant 0.33
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.18
ccsA 620752 p.Arg288Gly missense_variant 0.25
ccsA 620756 p.Asp289Gly missense_variant 0.31
ccsA 620773 p.Ile295Val missense_variant 0.24
rpoB 759808 c.2T>G start_lost 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 775603 p.Thr960Pro missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777427 p.Thr352Pro missense_variant 0.19
mmpL5 778907 c.-427C>G upstream_gene_variant 0.17
rpsL 781363 c.-197T>G upstream_gene_variant 0.27
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801287 p.Val160Gly missense_variant 0.35
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473945 n.288T>G non_coding_transcript_exon_variant 0.23
rrl 1473948 n.291C>A non_coding_transcript_exon_variant 0.17
rrl 1473953 n.296T>G non_coding_transcript_exon_variant 0.45
rrl 1473959 n.302T>G non_coding_transcript_exon_variant 0.22
rrl 1473966 n.309T>G non_coding_transcript_exon_variant 0.2
rrl 1473973 n.316T>G non_coding_transcript_exon_variant 0.22
rrl 1474452 n.795C>T non_coding_transcript_exon_variant 0.15
rrl 1474469 n.812T>G non_coding_transcript_exon_variant 0.2
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.5
rrl 1476574 n.2917A>C non_coding_transcript_exon_variant 0.33
fabG1 1674076 p.Thr213Pro missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918055 p.Ala39Gly missense_variant 0.18
tlyA 1918066 p.Ala43Pro missense_variant 0.27
ndh 2103235 c.-193C>G upstream_gene_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167859 c.2754T>G synonymous_variant 0.21
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169403 p.Thr404Ala missense_variant 0.17
PPE35 2170418 p.Met65Ile missense_variant 0.14
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 0.25
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.38
kasA 2518151 p.Ser13Arg missense_variant 0.36
kasA 2518605 p.Val164Gly missense_variant 0.21
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726265 p.Lys25Gln missense_variant 0.21
ahpC 2726269 p.Val26Gly missense_variant 0.19
ahpC 2726286 p.Gly32Arg missense_variant 0.19
pepQ 2859414 c.1005T>G synonymous_variant 0.25
ribD 2987316 p.Ala160Pro missense_variant 0.17
ribD 2987323 p.Val162Gly missense_variant 0.31
ribD 2987325 p.Ile163Val missense_variant 0.19
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyX 3068042 c.-97T>C upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087909 p.Thr364Pro missense_variant 0.22
fbiD 3339273 c.156T>G synonymous_variant 0.27
fbiD 3339279 c.162T>G synonymous_variant 0.19
fbiD 3339281 p.Ser55Leu missense_variant 0.19
fbiD 3339310 p.Asp65His missense_variant 0.17
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449087 p.Ala195Gly missense_variant 0.2
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
alr 3841253 c.168C>T synonymous_variant 1.0
ddn 3986919 p.Thr26Pro missense_variant 0.17
clpC1 4039484 c.1221T>G synonymous_variant 0.27
clpC1 4040517 p.Val63Ala missense_variant 0.96
embC 4240006 c.144A>C synonymous_variant 0.14
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242220 c.2358A>C synonymous_variant 0.28
embC 4242422 p.Trp854Gly missense_variant 0.21
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243347 p.Thr39Pro missense_variant 0.17
embA 4243350 p.Thr40Pro missense_variant 0.21
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246707 p.Gly65Ala missense_variant 0.12
embB 4247616 p.Glu368Gly missense_variant 0.17
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247805 p.Ala431Gly missense_variant 0.15
embB 4249403 p.Thr964Ala missense_variant 0.15
aftB 4267852 p.Gln329Lys missense_variant 0.15
aftB 4268776 p.Ser21Gly missense_variant 0.19
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269504 c.-668A>G upstream_gene_variant 0.24
ubiA 4269511 p.Val108Gly missense_variant 0.24
ubiA 4269514 p.Val107Gly missense_variant 0.25
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethR 4326907 c.-642C>G upstream_gene_variant 0.16
ethR 4327624 p.Glu26Lys missense_variant 0.18
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
gid 4407917 p.Arg96Cys missense_variant 1.0
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 1.0