TB-Profiler result

Run: SRR11972206
Summary

Run ID: SRR11972206

Sample name:

Date: 03-04-2023 05:31:53

Number of reads: 212995

Percentage reads mapped: 93.48

Strain: lineage1.1.3.1

Drug-resistance: HR-TB

Download CSV Download TXT Download PDF Download JSON
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
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 0.93
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.95
lineage1.1.3.1 Indo-Oceanic NA RD239 0.94
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
katG 2154256 p.Leu619Pro missense_variant 0.33 isoniazid
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 6533 p.Ala432Thr missense_variant 0.13
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
gyrA 9775 p.Asp825Val missense_variant 0.2
fgd1 491742 c.960T>C synonymous_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
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 0.92
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777572 c.909C>T synonymous_variant 0.88
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801263 p.Gly152Asp missense_variant 0.22
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1461056 c.12T>A synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472608 n.767delG non_coding_transcript_exon_variant 0.12
rrs 1472986 n.1141_1142insA non_coding_transcript_exon_variant 0.13
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.14
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.11
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.14
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.14
rrs 1473091 n.1246G>A non_coding_transcript_exon_variant 0.14
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.14
rrs 1473094 n.1249T>G non_coding_transcript_exon_variant 0.14
rrs 1473099 n.1254T>G non_coding_transcript_exon_variant 0.17
rrs 1473100 n.1255G>C non_coding_transcript_exon_variant 0.17
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.18
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.18
rrs 1473109 n.1264T>G non_coding_transcript_exon_variant 0.17
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.17
rrs 1473120 n.1275C>T non_coding_transcript_exon_variant 0.2
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.2
rrs 1473122 n.1277T>G non_coding_transcript_exon_variant 0.2
rrs 1473123 n.1278A>G non_coding_transcript_exon_variant 0.2
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.22
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.22
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.22
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.13
inhA 1674834 c.633C>A synonymous_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103213 c.-171G>A upstream_gene_variant 0.93
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167837 c.2772_2775delTGTT frameshift_variant 0.25
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167965 p.Ala883Gly missense_variant 0.2
PPE35 2167967 c.2646A>C synonymous_variant 0.2
PPE35 2167983 p.Gly877Asp missense_variant 0.88
PPE35 2168250 p.Gln788Arg missense_variant 0.2
PPE35 2169442 p.Ala391Ser missense_variant 0.13
PPE35 2169781 p.Gly278Arg missense_variant 0.2
PPE35 2169902 p.Leu237Phe missense_variant 0.27
PPE35 2169910 p.Asn235Tyr missense_variant 0.31
PPE35 2170300 p.Val105Ile missense_variant 0.93
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222746 p.Thr140Arg missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518315 c.201G>A synonymous_variant 0.25
kasA 2519000 p.Glu296Lys missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726254 p.Gly21Asp missense_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyA 3074632 c.-161C>A upstream_gene_variant 0.22
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 1.0
alr 3841253 c.168C>T synonymous_variant 0.96
alr 3841277 c.144C>T synonymous_variant 1.0
ddn 3986699 c.-145C>T upstream_gene_variant 0.11
clpC1 4039017 p.Ser563Tyr missense_variant 0.14
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4044098 p.Gly62Ser missense_variant 0.4
embC 4239714 c.-149C>T upstream_gene_variant 0.14
embC 4239953 p.Tyr31His missense_variant 0.13
embC 4240014 p.Pro51Leu missense_variant 0.18
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241823 p.Phe654Ser missense_variant 0.2
embC 4242050 p.Gln730* stop_gained 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.55
embA 4245134 p.Trp634* stop_gained 0.17
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246487 c.-27T>A upstream_gene_variant 0.4
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethR 4327751 p.Lys68Met missense_variant 0.18
whiB6 4338225 c.297C>T synonymous_variant 0.22
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 0.91
gid 4407873 c.330G>T synonymous_variant 1.0
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 1.0