TB-Profiler result

Run: ERR1873560
Summary

Run ID: ERR1873560

Sample name:

Date: 15-08-2022 11:08:25

Number of reads: 2940426

Percentage reads mapped: 84.44

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-TB

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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
lineage2 East-Asian Beijing RD105 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
gyrA 7582 p.Asp94Gly missense_variant 0.98 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.23 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.91 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288764 p.Thr160Ala missense_variant 1.0 pyrazinamide
pncA 2288943 p.Thr100Ile missense_variant 0.98 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.99 ethambutol
ethA 4327347 p.Gly43Cys missense_variant 1.0 ethionamide
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 491328 c.546C>G synonymous_variant 0.98
fgd1 491330 p.Lys183Met missense_variant 0.98
fgd1 491742 c.960T>C synonymous_variant 0.99
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 0.98
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764822 p.Asp485Tyr missense_variant 0.99
mmpL5 775592 c.2889G>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.12
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.12
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.14
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.13
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.17
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.23
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.22
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.25
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.29
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.29
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.24
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.18
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.17
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.17
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.17
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.12
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.11
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.23
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.25
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.26
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.25
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.28
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.28
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.25
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.25
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.17
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.19
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.16
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.19
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.22
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.26
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.22
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.33
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.29
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.19
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.14
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.22
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.3
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.32
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.32
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.4
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.39
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.48
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.42
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.38
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.38
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.32
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.28
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.18
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.12
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.12
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.12
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.13
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.12
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.12
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.12
rrl 1476547 n.2890C>T 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 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
thyA 3073806 c.666C>G synonymous_variant 0.26
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449315 p.Trp271* stop_gained 0.98
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.98
rpoA 3878641 c.-135delG upstream_gene_variant 0.1
clpC1 4038857 c.1848C>A synonymous_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4247717 p.Leu402Val missense_variant 1.0
embB 4249397 p.Ala962Pro missense_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338365 p.Cys53Arg missense_variant 0.98
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.97
gid 4407927 p.Glu92Asp missense_variant 0.98