TB-Profiler result

Run: ERR2510598
Summary

Run ID: ERR2510598

Sample name:

Date: 31-03-2023 18:49:54

Number of reads: 1018185

Percentage reads mapped: 99.49

Strain: lineage4.6;lineage3

Drug-resistance: Pre-XDR-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 0.16
lineage4 Euro-American LAM;T;S;X;H None 0.84
lineage4.6 Euro-American T;LAM None 0.8
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
gyrA 7582 p.Asp94Ala missense_variant 0.45 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.88 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embA 4243221 c.-12C>T upstream_gene_variant 0.82 ethambutol
embB 4247429 p.Met306Val missense_variant 0.21 ethambutol
gid 4407731 c.471delG frameshift_variant 0.21 streptomycin
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
ccsA 620577 c.687C>A synonymous_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 0.16
rpoC 763644 p.Met92Thr missense_variant 0.75
rpoC 764208 p.Val280Ala missense_variant 0.1
rpoC 764832 p.Glu488Gly missense_variant 0.77
rpoC 766597 c.3228C>G synonymous_variant 0.75
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.14
mmpL5 776169 p.Gly771Ala missense_variant 0.12
mmpL5 777820 c.661C>T synonymous_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416952 p.Glu132Asp missense_variant 0.22
embR 1417425 c.-78C>T upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154699 p.Gln471His missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 0.35
PPE35 2167926 p.Leu896Ser missense_variant 0.17
PPE35 2168080 p.Thr845Ala missense_variant 0.89
PPE35 2170198 p.Ala139Thr missense_variant 0.83
PPE35 2170792 c.-180T>C upstream_gene_variant 0.76
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.15
pncA 2289365 c.-125delC upstream_gene_variant 0.28
ahpC 2726040 c.-153G>A upstream_gene_variant 0.11
ahpC 2726105 c.-88G>A upstream_gene_variant 0.19
folC 2746993 c.606C>T synonymous_variant 0.88
Rv2752c 3065194 c.997dupC frameshift_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 0.21
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3613057 c.60G>T synonymous_variant 0.82
alr 3841473 c.-53G>A upstream_gene_variant 0.15
embC 4242075 p.Arg738Gln missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.17
gid 4407798 c.404dupT frameshift_variant 0.83