TB-Profiler result

Run: SRR6896469
Summary

Run ID: SRR6896469

Sample name:

Date: 04-04-2023 18:07:06

Number of reads: 457116

Percentage reads mapped: 98.99

Strain: lineage4.3.4.2.1

Drug-resistance: Other

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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 0.99
lineage4.3 Euro-American (LAM) mainly-LAM None 0.94
lineage4.3.4 Euro-American (LAM) LAM RD174 0.96
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.95
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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
pncA 2289024 c.217delG frameshift_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 6140 p.Val301Leu missense_variant 0.97
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9099 p.Leu600Ile missense_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491527 p.Trp249Arg missense_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 0.17
mshA 575482 c.135C>A synonymous_variant 0.11
mshA 575533 c.186C>T synonymous_variant 0.12
mshA 575675 p.Arg110Cys missense_variant 0.11
mshA 576275 p.Asp310Tyr missense_variant 0.22
ccsA 619829 c.-62G>T upstream_gene_variant 0.25
ccsA 620251 p.Gly121Trp missense_variant 0.17
rpoB 761152 p.Leu449Gln missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 0.97
rpoC 765454 c.2085C>T synonymous_variant 0.11
rpoC 766317 p.Met983Lys missense_variant 0.11
rpoC 766787 p.Glu1140* stop_gained 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778214 p.Ser89Arg missense_variant 0.12
mmpS5 778631 p.Leu92Trp missense_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801411 c.603C>A synonymous_variant 0.12
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.33
Rv1258c 1407405 c.-65C>T upstream_gene_variant 0.18
embR 1417174 c.174C>T synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474518 n.861C>T non_coding_transcript_exon_variant 0.11
rpsA 1833407 c.-135T>A upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102911 c.132G>T synonymous_variant 0.2
katG 2153901 p.Phe737Leu missense_variant 0.17
katG 2154020 p.Phe698Leu missense_variant 0.11
katG 2155471 p.Arg214Pro missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289772 c.-531C>A upstream_gene_variant 0.18
kasA 2519093 p.Arg327Ser missense_variant 0.12
eis 2714695 p.Glu213Gly missense_variant 0.13
folC 2746405 p.Phe398Leu missense_variant 0.12
pepQ 2860047 c.371delC frameshift_variant 0.11
ribD 2986715 c.-124T>A upstream_gene_variant 0.1
Rv2752c 3065929 p.Gly88Val missense_variant 0.14
Rv2752c 3065953 p.Thr80Asn missense_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 0.91
Rv3236c 3612496 c.621C>G synonymous_variant 0.2
alr 3840719 c.702A>G synonymous_variant 0.96
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039071 p.Pro545Gln missense_variant 0.15
embC 4242332 p.Gly824Trp missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244407 p.Thr392Met missense_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.11
embB 4246548 p.Pro12Gln missense_variant 0.11
embB 4246555 c.42G>C synonymous_variant 0.12
embB 4246556 p.Ala15Pro missense_variant 0.12
embB 4246563 p.Leu17Trp missense_variant 0.11
embB 4246567 c.54G>T synonymous_variant 0.12
embB 4247623 c.1114delC frameshift_variant 0.1
embB 4248907 c.2394G>T synonymous_variant 0.11
aftB 4267225 p.Ile538Phe missense_variant 0.11
aftB 4268393 c.444G>T synonymous_variant 0.14
ubiA 4269975 c.-142G>A upstream_gene_variant 0.11
whiB6 4338406 p.Asp39Gly missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
fbiC 1305494 c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN frameshift_variant&stop_lost&splice_region_variant 1.0