TB-Profiler result

Run: SRR14088383

Summary

Run ID: SRR14088383

Sample name:

Date: 03-04-2023 09:46:54

Number of reads: 3781712

Percentage reads mapped: 99.57

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 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761082 c.1279_1284delACCAGC conservative_inframe_deletion 1.0 rifampicin
embB 4247431 p.Met306Ile missense_variant 0.9 ethambutol
embB 4247496 p.Asp328Gly missense_variant 0.96 ethambutol
katG 2148916 c.-3066_*4972del transcript_ablation 1.0 isoniazid
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
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.21
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 764931 p.Ala521Asp missense_variant 0.93
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779314 c.328dupG frameshift_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473083 n.1238G>T non_coding_transcript_exon_variant 0.18
rrl 1473756 n.99G>A non_coding_transcript_exon_variant 0.17
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
eis 2714491 p.Asp281Gly missense_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
Rv2752c 3065607 c.585C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.32
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 0.12
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269306 p.Phe176Leu missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407555 c.648A>G synonymous_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408099 p.Leu35Pro missense_variant 1.0