TB-Profiler result

Run: SRR3675532
Summary

Run ID: SRR3675532

Sample name:

Date: 04-04-2023 05:34:20

Number of reads: 2641268

Percentage reads mapped: 80.59

Strain: lineage3.1.3

Drug-resistance: HR-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 1.0
lineage3.1.3 East-African-Indian CAS RD750 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 2155648 p.Tyr155Cys missense_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.24
rpoB 761150 c.1344A>C synonymous_variant 0.11
rpoB 761165 c.1359G>C synonymous_variant 0.12
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765222 p.Ala618Val 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
Rv1258c 1406613 p.Glu243Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.12
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.13
rrl 1473805 n.148G>T non_coding_transcript_exon_variant 0.12
rrl 1475220 n.1564delC non_coding_transcript_exon_variant 0.12
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.12
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.15
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.15
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.15
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.13
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.12
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.17
fabG1 1673346 c.-94C>G upstream_gene_variant 0.2
fabG1 1673349 c.-91G>C upstream_gene_variant 0.19
fabG1 1673357 c.-83G>A upstream_gene_variant 0.15
fabG1 1673359 c.-81T>C upstream_gene_variant 0.15
fabG1 1673361 c.-79C>G upstream_gene_variant 0.15
rpsA 1834159 c.618G>A synonymous_variant 1.0
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 2170048 p.Leu189Val missense_variant 0.26
PPE35 2170053 p.Thr187Ser missense_variant 0.29
Rv1979c 2222732 c.432delT frameshift_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.25
thyA 3074645 c.-174T>G upstream_gene_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448489 c.-15C>A upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612831 p.Asp96Tyr missense_variant 0.12
rpoA 3878434 p.Pro25Gln missense_variant 0.12
clpC1 4039348 p.Arg453Gly missense_variant 0.11
embC 4242075 p.Arg738Gln missense_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.16
embB 4246555 c.42G>C synonymous_variant 0.12
embB 4246556 p.Ala15Pro missense_variant 0.12
embB 4249195 c.2682C>A synonymous_variant 1.0
aftB 4267885 p.Ser318Cys missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408175 p.Ala10Pro missense_variant 1.0