TB-Profiler result

Run: SRR12882370
Summary

Run ID: SRR12882370

Sample name:

Date: 03-04-2023 07:31:28

Number of reads: 936958

Percentage reads mapped: 99.16

Strain:

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
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.2.2 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 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
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 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
rpoB 760589 c.783C>T synonymous_variant 0.11
rpoB 762041 p.His745Gln missense_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 767105 p.Asn1246Asp missense_variant 0.12
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 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472005 n.160T>C non_coding_transcript_exon_variant 1.0
rrl 1473619 n.-39G>C upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155356 c.756T>C synonymous_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2169071 c.1464_1541delGGCGGTGACGACGCCGGCCAACGTTACCGTGGGTGCGTTTGATTTGCCGGGGTTGACGGTGCCGTCGTTGACGATTCC disruptive_inframe_deletion 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726014 c.-179A>G upstream_gene_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746303 c.1296C>T synonymous_variant 0.22
pepQ 2860162 p.Arg86Pro missense_variant 0.14
pepQ 2860420 c.-2T>A upstream_gene_variant 0.12
pepQ 2860576 c.-158A>G upstream_gene_variant 0.14
ribD 2986655 c.-184A>G upstream_gene_variant 0.12
ald 3086739 c.-81G>A upstream_gene_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
fbiA 3640702 c.161delA frameshift_variant 0.14
fbiA 3641393 c.852delA frameshift_variant 0.17
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240757 p.Thr299Ala missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243082 c.3221_3228delATCTGAAC frameshift_variant 0.18
embC 4243092 p.Leu1077Arg missense_variant 0.17
embC 4243095 p.Gly1078Val missense_variant 0.17
embA 4243099 c.-134G>C upstream_gene_variant 0.17
embA 4243102 c.-131G>T upstream_gene_variant 0.17
embC 4243103 p.Thr1081Pro missense_variant 0.17
embC 4243106 p.Arg1082Ser missense_variant 0.17
embC 4243107 c.3245_3246insGTTCAGAT frameshift_variant 0.17
embA 4244035 p.Gly268Asp missense_variant 0.18
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248192 p.Arg560His missense_variant 0.12
ubiA 4269215 p.Arg207Ser missense_variant 0.14
aftB 4269291 c.-455A>T upstream_gene_variant 0.12
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326148 c.1326G>T synonymous_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethR 4327057 c.-492G>A upstream_gene_variant 1.0
ethA 4327713 c.-240A>G upstream_gene_variant 1.0
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
PPE35 2169071 c.1463_1541delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNA frameshift_variant 1.0