TB-Profiler result

Run: SRR6797586
Summary

Run ID: SRR6797586

Sample name:

Date: 04-04-2023 16:13:17

Number of reads: 1007894

Percentage reads mapped: 98.87

Strain: lineage1.1.3.1

Drug-resistance: HR-TB

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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 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
katG 2156024 c.87delC frameshift_variant 0.17 isoniazid, 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
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
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 764541 p.Val391Gly missense_variant 0.12
rpoC 764543 p.Thr392Asp missense_variant 0.12
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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416554 p.Ser265Cys missense_variant 0.12
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.11
rrl 1474164 n.507C>T non_coding_transcript_exon_variant 0.12
rrl 1474174 n.517A>G non_coding_transcript_exon_variant 0.11
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.13
rrl 1474183 n.526T>C non_coding_transcript_exon_variant 0.13
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.13
rrl 1474202 n.545T>C non_coding_transcript_exon_variant 0.13
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.17
rrl 1474624 n.967G>A non_coding_transcript_exon_variant 0.14
rrl 1475240 n.1583C>T non_coding_transcript_exon_variant 1.0
inhA 1673660 c.-542C>T upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
Rv1979c 2222282 p.Ile295Val missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222418 p.Asp249Glu missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065926 p.Ala89Glu missense_variant 0.11
thyA 3074230 c.241delG frameshift_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087298 p.Met160Thr missense_variant 0.13
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474245 p.Gly80Val missense_variant 0.12
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568451 p.Val77Met missense_variant 0.14
alr 3841253 c.168C>T synonymous_variant 1.0
clpC1 4039775 c.930G>A synonymous_variant 0.13
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248612 p.Arg700His missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326007 c.1467T>C synonymous_variant 1.0
ethA 4328414 c.-941C>T upstream_gene_variant 0.15
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