TB-Profiler result

Run: ERR040140
Summary

Run ID: ERR040140

Sample name:

Date: 31-03-2023 08:48:17

Number of reads: 17075961

Percentage reads mapped: 99.13

Strain: lineage3

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
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
gyrA 7572 p.Ser91Pro missense_variant 0.98 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
katG 2154461 c.1650_1651insA frameshift_variant 0.99 isoniazid
eis 2715346 c.-14C>T upstream_gene_variant 0.99 kanamycin, amikacin
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 491742 c.960T>C synonymous_variant 1.0
rpoB 762249 p.Leu815Val missense_variant 0.17
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.37
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764725 p.Phe452Leu missense_variant 0.18
rpoC 767305 p.Tyr1312* stop_gained 0.21
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461019 c.-26C>A upstream_gene_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472857 n.1012A>G non_coding_transcript_exon_variant 1.0
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.18
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.2
inhA 1674952 p.Pro251Ala missense_variant 0.15
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 2169866 c.747G>C synonymous_variant 0.4
PPE35 2170156 p.Ala153Pro missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
eis 2714366 p.Val323Leu missense_variant 0.2
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726116 c.-77T>G upstream_gene_variant 0.9
folC 2746186 c.1413G>C synonymous_variant 0.24
pepQ 2859381 c.1038C>G synonymous_variant 0.2
ribD 2987307 p.Ala157Pro missense_variant 0.22
Rv2752c 3064552 p.Arg547Pro missense_variant 0.22
Rv2752c 3064741 p.Gly484Ala missense_variant 0.23
thyA 3073806 c.666C>G synonymous_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.22
fbiB 3642098 c.564G>A synonymous_variant 1.0
alr 3840636 p.Pro262Gln missense_variant 1.0
rpoA 3878622 c.-115C>G upstream_gene_variant 0.99
clpC1 4038857 c.1848C>A synonymous_variant 0.23
clpC1 4039932 p.Gly258Val missense_variant 0.29
embC 4242075 p.Arg738Gln missense_variant 0.99
embC 4242425 p.Arg855Gly missense_variant 0.28
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.35
embA 4244375 c.1143C>G synonymous_variant 0.32
embA 4245883 p.Gly884Asp missense_variant 1.0
embB 4247501 p.Phe330Ile missense_variant 0.39
ubiA 4269317 p.Ser173Ala missense_variant 0.99
ubiA 4269529 p.Ala102Gly missense_variant 0.2
ethA 4326230 p.Asp415Gly missense_variant 1.0
ethA 4327672 c.-199G>A upstream_gene_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0