TB-Profiler result

Run: ERR4818288
Summary

Run ID: ERR4818288

Sample name:

Date: 01-04-2023 15:28:27

Number of reads: 384897

Percentage reads mapped: 95.73

Strain: lineage3

Drug-resistance: HR-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
katG 2154205 p.Ala636Glu missense_variant 0.1 isoniazid
katG 2155169 c.942delC frameshift_variant 0.12 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
gyrB 6162 p.Ile308Thr missense_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8283 p.Ile328Val missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575259 c.-89G>A upstream_gene_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.38
rpoB 759615 c.-192A>C upstream_gene_variant 0.18
rpoB 760511 c.705G>A synonymous_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763911 p.Leu181Pro missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779647 c.-742G>A upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781699 p.Ser47* stop_gained 0.12
fbiC 1305494 p.Ala855Val missense_variant 0.17
atpE 1460950 c.-95T>C upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472954 n.1110delC non_coding_transcript_exon_variant 0.2
rrs 1472958 n.1113_1114insC non_coding_transcript_exon_variant 0.22
rrs 1472969 n.1125_1126delCG non_coding_transcript_exon_variant 0.2
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.4
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.2
rrs 1472977 n.1132G>T non_coding_transcript_exon_variant 0.2
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.18
rrs 1472987 n.1141_1142insA non_coding_transcript_exon_variant 0.22
rrs 1472989 n.1145A>C non_coding_transcript_exon_variant 0.22
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.2
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.2
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.2
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.2
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.2
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 0.2
rpsA 1834668 p.Ala376Val missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170096 p.Arg173Trp missense_variant 0.25
Rv1979c 2223060 c.105T>A synonymous_variant 0.12
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
ahpC 2726350 p.Trp53Leu missense_variant 0.25
ahpC 2726519 c.327G>A synonymous_variant 0.17
folC 2746893 p.Arg236Cys missense_variant 0.25
Rv2752c 3065930 p.Gly88Trp missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474190 p.Ser62Thr missense_variant 0.15
fbiB 3640731 c.-804C>T upstream_gene_variant 0.18
fbiB 3642367 p.Ala278Val missense_variant 0.15
alr 3841194 p.Arg76Leu missense_variant 0.12
clpC1 4039731 p.Leu325His missense_variant 0.12
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4268003 c.834G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0