TB-Profiler result

Run: SRR11972350
Summary

Run ID: SRR11972350

Sample name:

Date: 03-04-2023 05:38:16

Number of reads: 2355799

Percentage reads mapped: 98.79

Strain: lineage2.2.1

Drug-resistance: MDR-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 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
rpoB 761139 p.His445Asp missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.95 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.98 ethambutol
embB 4249583 p.Asp1024Asn 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
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761773 p.His656Pro 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
fbiC 1304449 p.Ala507Thr missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.11
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.19
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.2
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.21
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.21
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.16
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.17
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.2
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.21
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.2
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.12
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.16
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.16
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.17
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.17
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.29
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.17
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.19
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.14
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.14
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.17
rrl 1474256 n.599T>C non_coding_transcript_exon_variant 0.1
rrl 1474733 n.1076C>T non_coding_transcript_exon_variant 0.2
rrl 1475218 n.1561C>T non_coding_transcript_exon_variant 0.22
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.13
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.13
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.17
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.18
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.12
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.1
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.25
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.23
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.27
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.24
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.23
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.23
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.13
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
PPE35 2170159 p.Ala152Ser missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859592 p.Ala276Glu missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475007 p.Phe334Ser missense_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
clpC1 4038253 p.Phe818Leu missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.29
embB 4246548 p.Pro12Gln missense_variant 0.24
embB 4246555 c.42G>C synonymous_variant 0.37
embB 4246556 p.Ala15Pro missense_variant 0.38
embB 4246563 p.Leu17Trp missense_variant 0.21
embB 4246567 c.54G>T synonymous_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4328315 c.-842C>T upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338600 c.-79T>G upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0