TB-Profiler result

Run: SRR998647
Summary

Run ID: SRR998647

Sample name:

Date: 04-04-2023 23:29:54

Number of reads: 3128812

Percentage reads mapped: 99.23

Strain: lineage6.3.1

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download PDF Download JSON
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
lineage6 West-Africa 2 AFRI_1 RD702 0.99
lineage6.3 West-Africa 2 AFRI_1 RD702 0.14
lineage6.3.1 West-Africa 2 AFRI_1 RD702 0.11
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 7570 p.Ala90Val missense_variant 0.2 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.15 rifampicin
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 6446 p.Ala403Ser missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8493 p.Leu398Phe missense_variant 0.85
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9539 c.2238C>T synonymous_variant 0.85
gyrA 9591 p.Gly764Arg missense_variant 0.12
fgd1 491668 p.Lys296Glu missense_variant 0.99
fgd1 491742 c.960T>C synonymous_variant 0.99
rpoB 760969 p.Ser388Leu missense_variant 1.0
rpoB 761723 p.Glu639Asp missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.96
rpoC 766231 c.2862T>C synonymous_variant 0.78
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
Rv1258c 1406685 p.Val219Ala missense_variant 0.88
embR 1416633 p.Leu239Val missense_variant 0.88
atpE 1461251 c.207G>T synonymous_variant 0.95
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674434 p.Val78Ala missense_variant 0.98
inhA 1674839 p.Ala213Val missense_variant 0.93
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102694 p.Val117Ile missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155503 c.609C>T synonymous_variant 0.97
katG 2156366 c.-255G>A upstream_gene_variant 0.16
PPE35 2167926 p.Leu896Ser missense_variant 0.99
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222852 p.Ala105Thr missense_variant 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
thyA 3074393 p.Arg27Cys missense_variant 0.86
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086739 c.-80delA upstream_gene_variant 0.93
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 0.99
Rv3083 3449781 c.1278G>A synonymous_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612143 p.Arg325His missense_variant 0.85
fbiB 3642071 c.537C>T synonymous_variant 0.78
rpoA 3877696 p.Thr271Ile missense_variant 0.19
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241843 p.Leu661Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 0.96
embA 4244379 p.Pro383Ser missense_variant 0.97
embB 4246864 c.351C>T synonymous_variant 0.98
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247816 p.Val435Ile missense_variant 0.82
aftB 4268477 c.360C>T synonymous_variant 0.2
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269522 c.-686C>T upstream_gene_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326465 p.Ile337Val missense_variant 1.0
whiB6 4338478 p.Phe15Ser missense_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.98
gid 4408034 p.Glu57Lys missense_variant 0.85