TB-Profiler result

Run: SRR19428526
Summary

Run ID: SRR19428526

Sample name:

Date: 03-04-2023 21:39:08

Number of reads: 633163

Percentage reads mapped: 99.62

Strain: lineage4.2.2.2;lineage3.1.1;lineage2.2.1

Drug-resistance: RR-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
lineage3 East-African-Indian CAS RD750 0.58
lineage4 Euro-American LAM;T;S;X;H None 0.29
lineage4.2 Euro-American H;T;LAM None 0.22
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.16
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.58
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.13
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.54
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.18
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.26
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 761155 p.Ser450Leu missense_variant 0.13 rifampicin
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8688 p.Ala463Ser missense_variant 0.41
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.65
mshA 575907 p.Ala187Val missense_variant 0.15
mshA 576077 c.730C>T synonymous_variant 0.2
ccsA 620625 p.Ile245Met missense_variant 0.14
rpoB 759746 c.-61C>T upstream_gene_variant 0.6
rpoC 762434 c.-936T>G upstream_gene_variant 0.71
rpoC 763031 c.-339T>C upstream_gene_variant 0.81
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.88
mmpL5 776182 p.Asp767Asn missense_variant 0.26
mmpS5 779615 c.-710C>G upstream_gene_variant 0.21
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406262 c.1076_1078delCCG disruptive_inframe_deletion 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475259 n.1602T>G non_coding_transcript_exon_variant 0.23
inhA 1674415 c.216delC frameshift_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.91
PPE35 2167926 p.Leu896Ser missense_variant 0.78
PPE35 2170011 p.Arg201Gln missense_variant 0.11
PPE35 2170461 p.Gly51Glu missense_variant 0.75
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.54
pncA 2289365 c.-125delC upstream_gene_variant 0.59
kasA 2518415 p.Pro101Ser missense_variant 0.12
kasA 2518594 c.480C>T synonymous_variant 0.1
eis 2714526 c.805_806delAC frameshift_variant 0.14
ahpC 2726105 c.-88G>A upstream_gene_variant 0.62
Rv2752c 3065711 p.Gly161Ser missense_variant 0.19
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.3
thyX 3067704 p.Tyr81Phe missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449054 p.Gly184Asp missense_variant 0.13
Rv3083 3449245 p.Ile248Val missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.16
embC 4240172 p.Val104Met missense_variant 0.33
embC 4241562 p.Arg567His missense_variant 0.52
embC 4242075 p.Arg738Gln missense_variant 0.65
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247161 c.648G>C synonymous_variant 0.11
embB 4249673 p.Ser1054Pro missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 0.35
aftB 4268605 p.Arg78Cys missense_variant 0.12
whiB6 4338367 p.Leu52Gln missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.81
gid 4407859 p.Val115Ala missense_variant 0.13
gid 4407862 p.Ile114Thr missense_variant 0.12
gid 4407927 p.Glu92Asp missense_variant 0.25