TB-Profiler result

Run: ERR2513160
Summary

Run ID: ERR2513160

Sample name:

Date: 31-03-2023 19:29:55

Number of reads: 2782137

Percentage reads mapped: 98.37

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
gyrB 6575 p.Arg446Cys missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761277 p.Ile491Phe missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.1 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288869 p.Val125Phe missense_variant 1.0 pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol
embB 4247729 p.Gly406Ser missense_variant 1.0 ethambutol
ethA 4326721 c.752dupG frameshift_variant 1.0 ethionamide, ethionamide
gid 4407618 p.Tyr195* stop_gained 1.0 streptomycin
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 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761276 c.1470G>T 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 764944 p.His525Gln missense_variant 1.0
rpoC 766582 c.3213C>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.15
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.13
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.18
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.15
rrs 1472686 n.841G>T non_coding_transcript_exon_variant 0.1
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.11
rrs 1472690 n.845C>T non_coding_transcript_exon_variant 0.11
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.14
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.11
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.14
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.1
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.11
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.13
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.12
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.12
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.17
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.14
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.12
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.16
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.11
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.27
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.23
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.22
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.21
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.17
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.17
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.17
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.15
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.15
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.15
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.15
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.11
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.13
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.12
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.12
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.12
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.12
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.12
rrl 1475892 n.2235A>G non_coding_transcript_exon_variant 0.96
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.19
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.23
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.17
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.18
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.22
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.13
rrl 1476506 n.2849T>C non_coding_transcript_exon_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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
Rv2752c 3065011 p.Met394Arg missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841473 c.-53G>A upstream_gene_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0