TB-Profiler result

Run: SRR19428529
Summary

Run ID: SRR19428529

Sample name:

Date: 03-04-2023 21:39:21

Number of reads: 1474028

Percentage reads mapped: 99.51

Strain: lineage4.2.2.2;lineage3.1.1;lineage1.1.2

Drug-resistance: MDR-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
lineage3 East-African-Indian CAS RD750 0.31
lineage4 Euro-American LAM;T;S;X;H None 0.37
lineage1 Indo-Oceanic EAI RD239 0.24
lineage4.2 Euro-American H;T;LAM None 0.37
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.24
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.36
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.33
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.22
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.31
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.39
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
rpoB 761100 p.Gln432Glu missense_variant 0.3 rifampicin
rpsL 781822 p.Lys88Met missense_variant 0.4 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.33 isoniazid
embB 4248003 p.Gln497Arg missense_variant 0.27 ethambutol
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 0.15
gyrB 6124 c.885C>T synonymous_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.24
gyrA 8688 p.Ala463Ser missense_variant 0.32
gyrA 9143 c.1842T>C synonymous_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.54
mshA 576077 c.730C>T synonymous_variant 0.4
rpoB 759746 c.-61C>T upstream_gene_variant 0.31
rpoB 760490 c.684C>T synonymous_variant 0.12
rpoB 761248 p.Glu481Ala missense_variant 0.35
rpoB 761489 c.1683G>A synonymous_variant 0.33
rpoB 762201 p.Lys799Gln missense_variant 0.13
rpoC 762434 c.-936T>G upstream_gene_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_variant 0.62
rpoC 763884 p.Ala172Val missense_variant 0.21
rpoC 763886 c.517C>A synonymous_variant 0.21
rpoC 765171 p.Pro601Leu missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.53
mmpR5 779303 p.Arg105His missense_variant 0.21
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303051 p.Val41Met missense_variant 0.17
Rv1258c 1406349 p.Ile331Ser missense_variant 0.1
embR 1417019 p.Cys110Tyr missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475259 n.1602T>G non_coding_transcript_exon_variant 0.42
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.5
PPE35 2167926 p.Leu896Ser missense_variant 0.73
PPE35 2167983 p.Gly877Asp missense_variant 0.25
PPE35 2170461 p.Gly51Glu missense_variant 0.24
Rv1979c 2222308 p.Asp286Gly missense_variant 0.17
Rv1979c 2223136 p.Ala10Val missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288911 p.Glu111* stop_gained 0.34
pncA 2289047 c.195C>T synonymous_variant 0.2
pncA 2289365 c.-125delC upstream_gene_variant 0.32
kasA 2518132 c.18C>T synonymous_variant 0.28
ahpC 2726051 c.-142G>A upstream_gene_variant 0.18
ahpC 2726105 c.-88G>A upstream_gene_variant 0.27
ahpC 2726534 c.342C>T synonymous_variant 0.11
Rv2752c 3064632 c.1560C>T synonymous_variant 0.37
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.35
ald 3086742 c.-78A>C upstream_gene_variant 0.53
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.44
fprA 3474700 p.Gly232Ser missense_variant 0.12
fprA 3475159 p.Asn385Asp missense_variant 0.17
rpoA 3878641 c.-135delG upstream_gene_variant 0.22
clpC1 4040517 p.Val63Ala missense_variant 0.32
embC 4240671 p.Thr270Ile missense_variant 0.11
embC 4241042 p.Asn394Asp missense_variant 0.22
embC 4241562 p.Arg567His missense_variant 0.24
embC 4242075 p.Arg738Gln missense_variant 0.36
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.32
embA 4244167 p.Ala312Val missense_variant 0.22
embA 4245969 p.Pro913Ser missense_variant 0.2
embB 4247646 p.Glu378Ala missense_variant 0.26
embB 4249673 p.Ser1054Pro missense_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 0.12
ubiA 4269387 p.Glu149Asp missense_variant 0.31
ubiA 4269469 p.Pro122Gln missense_variant 0.12
aftB 4269606 c.-770T>C upstream_gene_variant 0.29
ethA 4326432 p.Leu348Phe missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.26
gid 4407588 c.615A>G synonymous_variant 0.76
gid 4407873 c.330G>T synonymous_variant 0.13