TB-Profiler result

Run: SRR7517784
Summary

Run ID: SRR7517784

Sample name:

Date: 04-04-2023 19:38:08

Number of reads: 1848729

Percentage reads mapped: 98.96

Strain: lineage1.1.3.3

Drug-resistance: Other

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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 0.99
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.3.3 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
gid 4407851 c.351delG frameshift_variant 1.0 streptomycin
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 8297 c.996C>T 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
gyrA 9654 p.Arg785Ser missense_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760043 c.237C>T synonymous_variant 0.5
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763193 c.-177C>A upstream_gene_variant 0.17
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764189 p.Ala274Thr missense_variant 0.12
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
rpoC 766506 p.Ile1046Thr missense_variant 1.0
rpoC 766755 p.Glu1129Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776045 c.2436G>T synonymous_variant 0.2
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778612 c.-132C>A upstream_gene_variant 0.15
mmpL5 779238 c.-758G>T upstream_gene_variant 0.29
mmpS5 779549 c.-644G>T upstream_gene_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303608 p.Lys226Asn missense_variant 0.13
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417024 p.Asn108Lys missense_variant 0.12
embR 1417192 c.156C>A synonymous_variant 0.13
embR 1417238 p.Ala37Gly missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474793 n.1136C>A non_coding_transcript_exon_variant 0.33
rrl 1475049 n.1392C>T non_coding_transcript_exon_variant 1.0
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.22
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.25
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.25
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.25
rpsA 1833641 p.Asn34Asp missense_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155953 c.159C>A synonymous_variant 0.2
katG 2156146 c.-35A>G upstream_gene_variant 1.0
katG 2156233 c.-122C>T upstream_gene_variant 0.33
PPE35 2167703 p.Leu970Phe missense_variant 0.25
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168430 p.Gly728Val missense_variant 0.5
PPE35 2168570 p.Asn681Lys missense_variant 0.25
PPE35 2168594 c.2019C>T synonymous_variant 0.33
PPE35 2170048 p.Leu189Val missense_variant 0.17
PPE35 2170053 p.Thr187Ser missense_variant 0.14
PPE35 2170726 c.-114G>T upstream_gene_variant 0.12
Rv1979c 2222184 p.Trp327Cys missense_variant 0.14
Rv1979c 2222211 c.954G>T synonymous_variant 0.14
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222569 p.Ala199Glu missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223361 c.-197C>A upstream_gene_variant 0.18
ahpC 2726051 c.-142G>A upstream_gene_variant 0.92
folC 2746365 c.1234C>T synonymous_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
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
rpoA 3877518 p.Trp330Cys missense_variant 0.13
rpoA 3878077 p.Arg144His missense_variant 0.13
clpC1 4040241 p.Thr155Ile missense_variant 0.12
clpC1 4040250 p.Glu152Gly missense_variant 0.11
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 0.95
embB 4246797 p.Gly95Asp missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4266975 p.Pro621Arg missense_variant 1.0
aftB 4267234 p.Asp535Tyr missense_variant 0.5
aftB 4267431 p.Ser469Leu missense_variant 0.88
ubiA 4269387 p.Glu149Asp missense_variant 0.94
aftB 4269606 c.-770T>C upstream_gene_variant 0.97
ethA 4327401 p.Asp25Tyr missense_variant 0.4
ethR 4327559 p.Ser4Tyr missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.9
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