TB-Profiler result

Run: ERR4831532
Summary

Run ID: ERR4831532

Sample name:

Date: 01-04-2023 20:59:41

Number of reads: 1657195

Percentage reads mapped: 44.85

Strain: lineage2.2.2

Drug-resistance: MDR-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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.98 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.97 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289202 p.Cys14Arg missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326333 p.Ala381Pro missense_variant 1.0 ethionamide
gid 4407967 p.Leu79Ser missense_variant 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
rpoC 762836 c.-534C>G upstream_gene_variant 0.19
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.12
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.12
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.45
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.46
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.47
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.48
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.48
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.46
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.46
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.15
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.16
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.25
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.25
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.26
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.26
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.25
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.32
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.34
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.32
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.32
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.32
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.31
rrs 1473124 n.1279A>T non_coding_transcript_exon_variant 0.13
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.16
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.16
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.16
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.17
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.17
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.17
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.17
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.17
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.18
rrs 1473179 n.1334C>T non_coding_transcript_exon_variant 0.19
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.19
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.18
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.1
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.1
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.12
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.12
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.11
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.38
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.39
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.42
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.4
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.35
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153933 p.Ala727Ser missense_variant 0.23
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.22
PPE35 2169866 c.747G>C synonymous_variant 0.29
Rv1979c 2221939 p.Arg409Gln missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2987307 p.Ala157Pro missense_variant 0.14
thyA 3073806 c.666C>G synonymous_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878641 c.-135delG upstream_gene_variant 0.17
clpC1 4038857 c.1848C>A synonymous_variant 0.24
embC 4239842 c.-21C>A upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.23
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269089 p.Ala249Thr missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0