TB-Profiler result

Run: SRR1162898
Summary

Run ID: SRR1162898

Sample name:

Date: 02-04-2023 23:24:25

Number of reads: 1324804

Percentage reads mapped: 98.72

Strain: 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 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 7581 p.Asp94Tyr missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761109 p.Asp435Tyr missense_variant 0.96 rifampicin
rpoB 761137 p.Thr444Ile missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155322 p.Ala264Thr missense_variant 0.12 isoniazid
pncA 2288713 c.527_528dupGC frameshift_variant 0.9 pyrazinamide, pyrazinamide
ethA 4326718 c.754_755dupGC frameshift_variant 0.91 ethionamide, ethionamide
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 5120 c.-120T>C upstream_gene_variant 0.1
gyrB 5754 p.Arg172Leu missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9596 c.2295G>T synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576438 p.Ala364Val missense_variant 1.0
mshA 576530 p.Val395Phe missense_variant 0.14
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764181 p.Asp271Gly 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
embR 1416920 p.Arg143Lys missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834985 c.1445dupG frameshift_variant&stop_lost&splice_region_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102528 p.Thr172Ile missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155309 p.Gly268Asp missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170769 c.-157C>T upstream_gene_variant 1.0
Rv1979c 2221727 p.Thr480Ala missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518975 c.861C>G synonymous_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 0.97
Rv2752c 3066117 c.74delA frameshift_variant 0.13
Rv2752c 3067124 c.-933G>A upstream_gene_variant 0.68
thyA 3073751 p.Tyr241His missense_variant 0.12
thyA 3074299 p.Glu58Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087251 c.434dupG frameshift_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640389 c.-154C>T upstream_gene_variant 0.84
embC 4242075 p.Arg738Gln missense_variant 1.0
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 1.0