TB-Profiler result

Run: SRR4035514

Summary

Run ID: SRR4035514

Sample name:

Date: 04-04-2023 07:08:35

Number of reads: 1392284

Percentage reads mapped: 99.54

Strain: lineage3

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 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
rpoB 761109 p.Asp435Tyr missense_variant 1.0 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 8056 p.Arg252Leu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760248 p.Met148Val missense_variant 0.22
rpoB 761195 c.1389G>A synonymous_variant 0.14
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762772 p.Asn989Ser missense_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763114 p.Gly1103Asp missense_variant 0.13
rpoC 763596 p.Glu76Gly missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776074 p.Val803Ile missense_variant 0.15
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776421 p.Asp687Val missense_variant 0.17
mmpL5 776725 p.Tyr586His missense_variant 0.15
mmpL5 776728 p.Phe585Leu missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303950 c.1020C>T synonymous_variant 0.13
fbiC 1305070 p.Asp714Asn missense_variant 0.14
embR 1417003 p.Phe115Leu missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471748 n.-98C>T upstream_gene_variant 0.18
rrs 1472199 n.354C>T non_coding_transcript_exon_variant 0.29
rrs 1473309 n.1464G>A non_coding_transcript_exon_variant 0.15
rrl 1475197 n.1540G>T non_coding_transcript_exon_variant 0.29
rrl 1476388 n.2731T>A non_coding_transcript_exon_variant 0.18
rrl 1476400 n.2743G>A non_coding_transcript_exon_variant 0.2
rrl 1476695 n.3041delG non_coding_transcript_exon_variant 0.17
rrl 1476711 n.3054G>T non_coding_transcript_exon_variant 0.17
inhA 1673691 c.-511G>A upstream_gene_variant 0.14
fabG1 1673699 p.Ser87Phe missense_variant 0.12
fabG1 1673732 p.Met98Lys missense_variant 0.12
inhA 1674952 p.Pro251Ala missense_variant 0.13
rpsA 1833353 c.-189C>T upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 0.96
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170251 p.Val121Gly missense_variant 0.12
Rv1979c 2223078 c.87C>A synonymous_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289295 c.-54T>C upstream_gene_variant 0.12
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2519320 c.1209delG frameshift_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 0.96
ribD 2986974 p.Ile46Val missense_variant 0.12
Rv2752c 3065434 p.Val253Glu missense_variant 0.13
Rv2752c 3065443 p.Asp250Gly missense_variant 0.14
Rv2752c 3065687 p.Gly169Ser missense_variant 0.12
thyX 3067703 c.243C>T synonymous_variant 0.2
thyA 3074424 c.48G>T synonymous_variant 1.0
thyA 3074474 c.-3A>G upstream_gene_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474372 c.366T>C synonymous_variant 0.13
whiB7 3568633 p.Pro16Arg missense_variant 0.12
Rv3236c 3613088 p.Glu10Gly missense_variant 0.12
rpoA 3877534 p.Val325Asp missense_variant 0.12
rpoA 3877553 p.Glu319* stop_gained 0.13
rpoA 3878191 p.Thr106Ile missense_variant 0.15
clpC1 4038234 p.Arg824Pro missense_variant 0.13
embC 4241460 p.Arg533Pro missense_variant 0.12
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245077 c.1845G>A synonymous_variant 0.14
aftB 4268058 p.Phe260Cys missense_variant 0.11
ethA 4327103 p.Gly124Asp missense_variant 0.17
ethA 4327477 c.-5delG upstream_gene_variant 0.14
ethA 4328212 c.-740delC upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408335 c.-133A>G upstream_gene_variant 0.13