TB-Profiler result

Run: SRR14088375
Summary

Run ID: SRR14088375

Sample name:

Date: 03-04-2023 09:46:25

Number of reads: 2059011

Percentage reads mapped: 99.76

Strain: lineage3

Drug-resistance: MDR-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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288953 p.Gly97Arg missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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 6470 p.Val411Met missense_variant 0.22
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
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760249 p.Met148Thr missense_variant 0.15
rpoB 760848 p.Thr348Ala missense_variant 0.1
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763497 p.Lys43Arg missense_variant 0.18
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473407 n.-251A>C upstream_gene_variant 0.18
rrl 1473409 n.-249T>A upstream_gene_variant 0.18
rrl 1473411 n.-247G>T upstream_gene_variant 0.18
rrl 1476608 n.2951C>T non_coding_transcript_exon_variant 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102604 c.439T>C synonymous_variant 0.1
katG 2154444 c.1668A>G synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167865 c.2748G>C synonymous_variant 0.11
PPE35 2167868 c.2745A>C synonymous_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222197 p.Ala323Val missense_variant 0.15
Rv1979c 2222256 c.909C>T synonymous_variant 0.15
Rv1979c 2222994 c.171C>T synonymous_variant 0.1
Rv1979c 2223070 p.Ile32Thr missense_variant 0.18
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
Rv2752c 3064989 c.1203G>A synonymous_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642877 p.Lys448Arg missense_variant 1.0
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