TB-Profiler result

Run: ERR4796348
Summary

Run ID: ERR4796348

Sample name:

Date: 01-04-2023 06:48:36

Number of reads: 2604546

Percentage reads mapped: 85.37

Strain: lineage2.2.1.2

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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
lineage2.2.1.2 East-Asian (Beijing) Beijing-RD142 RD105;RD207;RD181;RD142 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 7510 p.His70Arg missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288835 p.Asp136Gly missense_variant 1.0 pyrazinamide
folC 2747471 p.Ile43Thr missense_variant 1.0 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.32
mshA 576113 p.Arg256Gly missense_variant 0.37
mshA 576456 p.Val370Gly missense_variant 0.26
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_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 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.11
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.14
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.14
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.13
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.16
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.15
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.14
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.16
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.25
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.25
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.25
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.21
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.21
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.23
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.23
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.43
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.56
rrs 1472682 n.839_843delGGGAT non_coding_transcript_exon_variant 0.44
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.44
rrs 1472698 n.853A>C non_coding_transcript_exon_variant 0.44
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.46
rrs 1472705 n.860G>A non_coding_transcript_exon_variant 0.44
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.44
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.42
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.39
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.39
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.26
rrl 1473640 n.-18C>A upstream_gene_variant 0.19
rrl 1474398 n.742delG non_coding_transcript_exon_variant 0.33
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.19
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.21
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.25
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.22
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.23
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.23
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.22
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.23
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.11
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.13
rrl 1476572 n.2915G>T non_coding_transcript_exon_variant 0.12
rrl 1476573 n.2916A>G non_coding_transcript_exon_variant 0.12
rrl 1476594 n.2937C>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
ndh 2102312 c.730dupC frameshift_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.31
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.19
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.39
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.2
embC 4240409 p.Pro183Ala missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.27
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4327472 c.2T>C start_lost 1.0
whiB6 4338233 p.Ser97Pro 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