TB-Profiler result

Run: ERR2510541
Summary

Run ID: ERR2510541

Sample name:

Date: 31-03-2023 18:48:05

Number of reads: 550086

Percentage reads mapped: 99.56

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 0.99
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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 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 490636 c.-147G>C upstream_gene_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 759939 p.Pro45Ala missense_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764781 p.Ser471Thr missense_variant 0.12
rpoC 767009 p.Ser1214Ala missense_variant 0.17
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 1475514 n.1857G>C non_coding_transcript_exon_variant 0.29
rrl 1476295 n.2638C>A non_coding_transcript_exon_variant 0.2
inhA 1674389 p.Leu63Pro missense_variant 0.25
rpsA 1834578 p.Val346Asp missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102472 p.Glu191* stop_gained 0.12
ndh 2102528 p.Thr172Ile missense_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
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
pncA 2289680 c.-439T>A upstream_gene_variant 0.13
ahpC 2725972 c.-221A>T upstream_gene_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
Rv2752c 3064529 p.Val555Ile missense_variant 0.18
Rv2752c 3066115 p.Glu26Gly missense_variant 0.1
thyA 3074451 c.21G>C synonymous_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568857 c.-178C>T upstream_gene_variant 1.0
fbiB 3642672 p.Ala380Ser missense_variant 1.0
panD 4044023 c.259C>T synonymous_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245358 p.Ala709Val missense_variant 0.2
aftB 4268119 p.Ala240Thr missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407949 p.Asp85Ala missense_variant 1.0