TB-Profiler result

Run: SRR6982443

Summary

Run ID: SRR6982443

Sample name:

Date: 04-04-2023 18:37:35

Number of reads: 447747

Percentage reads mapped: 99.76

Strain: lineage4.9

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.9 Euro-American (H37Rv-like) T1 None 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 2155426 c.684_685dupCT frameshift_variant 0.12 isoniazid
pncA 2288749 p.Ala165Thr missense_variant 0.14 pyrazinamide
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 7043 p.Asn602Asp missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8765 c.1464C>T synonymous_variant 0.11
gyrA 9270 c.1970_1971delAC frameshift_variant 0.1
fgd1 491514 p.Asn244Lys missense_variant 0.2
mshA 576198 p.Leu284Pro missense_variant 0.18
rpoB 760564 p.Arg253Gln missense_variant 0.1
rpoB 762093 p.Ile763Phe missense_variant 0.25
rpoC 764499 p.Ser377Tyr missense_variant 0.18
rpoC 766844 p.Arg1159Ser missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776023 p.Val820Met missense_variant 0.12
mmpL5 776704 p.Asp593His missense_variant 0.15
mmpL5 777387 p.Gly365Asp missense_variant 0.13
mmpL5 778917 c.-437A>G upstream_gene_variant 0.11
mmpL5 778944 c.-465_-464insAC upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303484 p.Thr185Ser missense_variant 0.11
fbiC 1303615 c.688delC frameshift_variant 0.1
fbiC 1304184 c.1254G>T synonymous_variant 0.15
Rv1258c 1406326 c.1015C>A synonymous_variant 0.11
embR 1417436 c.-89T>C upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472111 n.266C>A non_coding_transcript_exon_variant 0.12
rrl 1473665 n.8T>C non_coding_transcript_exon_variant 0.12
rrl 1474850 n.1193C>T non_coding_transcript_exon_variant 0.2
rrl 1475573 n.1921delC non_coding_transcript_exon_variant 0.2
rrl 1476358 n.2701T>A non_coding_transcript_exon_variant 0.12
rpsA 1833364 c.-178C>T upstream_gene_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169402 p.Thr404Met missense_variant 1.0
PPE35 2170551 p.Ser21Phe missense_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289789 c.-548C>A upstream_gene_variant 0.2
kasA 2518151 p.Ser13Arg missense_variant 0.28
eis 2714472 c.861T>C synonymous_variant 0.15
ahpC 2725933 c.-260G>T upstream_gene_variant 0.13
ahpC 2726258 p.Asp22Glu missense_variant 0.23
ahpC 2726338 p.Val49Gly missense_variant 0.18
ahpC 2726425 p.Arg78His missense_variant 0.22
pepQ 2860105 p.Asp105Gly missense_variant 0.13
pepQ 2860150 p.Ala90Val missense_variant 0.12
Rv2752c 3065491 p.Ile234Arg missense_variant 1.0
thyA 3073806 c.666C>A synonymous_variant 0.12
ddn 3986894 c.51T>C synonymous_variant 0.11
clpC1 4038786 p.Gln640Arg missense_variant 0.11
embA 4245279 p.Arg683Cys missense_variant 0.14
embA 4245298 p.Pro689Gln missense_variant 0.15
embA 4245997 p.Trp922Leu missense_variant 0.13
embB 4247823 p.Thr437Asn missense_variant 0.11
embB 4249011 p.Leu833Pro missense_variant 0.11
aftB 4268824 p.Ser5Gly missense_variant 0.12
ethA 4326178 p.Met432Ile missense_variant 0.11
ethR 4328058 p.Glu170Asp missense_variant 0.1
ethA 4328407 c.-934G>A upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407916 p.Arg96His missense_variant 1.0