TB-Profiler result

Run: ERR2653102
Summary

Run ID: ERR2653102

Sample name:

Date: 31-03-2023 22:31:22

Number of reads: 574146

Percentage reads mapped: 99.47

Strain: lineage4.7

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.7 Euro-American (mainly T) T1;T5 None 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
gyrA 7572 p.Ser91Pro missense_variant 0.92 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764948 p.Leu527Val missense_variant 0.67 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
gid 4408100 c.102delG frameshift_variant 1.0 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
gyrB 6259 c.1020C>T synonymous_variant 0.1
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9458 c.2157A>G synonymous_variant 0.1
mshA 575896 c.549G>A synonymous_variant 0.13
ccsA 620852 p.Ala321Val missense_variant 0.12
rpoB 759940 p.Pro45Leu missense_variant 0.41
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775715 c.2766G>A synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.12
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918059 c.120C>A synonymous_variant 0.25
Rv1979c 2222097 c.1068G>A synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289070 p.Phe58Val missense_variant 1.0
ribD 2987346 p.Pro170Ser missense_variant 0.11
fbiD 3339652 p.Thr179Ala missense_variant 0.11
alr 3841071 p.Gly117Asp missense_variant 1.0
rpoA 3878601 c.-95delG upstream_gene_variant 0.59
clpC1 4040525 c.180C>T synonymous_variant 1.0
embC 4241591 p.Leu577Ile missense_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243977 p.Ala249Thr missense_variant 1.0
embB 4249732 c.3219C>G synonymous_variant 1.0
ethA 4327521 c.-48G>A upstream_gene_variant 0.12
ethA 4327523 c.-50G>C upstream_gene_variant 0.12
ethA 4327525 c.-52T>C upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407590 p.Ala205Thr missense_variant 1.0