TB-Profiler result

Run: SRR6257097
Summary

Run ID: SRR6257097

Sample name:

Date: 04-04-2023 13:26:12

Number of reads: 1056761

Percentage reads mapped: 95.6

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 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
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.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761095 p.Leu430Pro missense_variant 1.0 rifampicin
rpoB 761110 p.Asp435Gly missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288990 c.250_251delAG frameshift_variant 1.0 pyrazinamide, pyrazinamide
eis 2715369 c.-37G>T upstream_gene_variant 1.0 kanamycin
embB 4247553 p.Ser347Ile 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
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766087 c.2718C>A synonymous_variant 0.11
rpoC 766645 p.Glu1092Asp missense_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 1472598 n.753A>C non_coding_transcript_exon_variant 0.1
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.15
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.11
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.14
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.14
rrl 1475880 n.2223C>G non_coding_transcript_exon_variant 0.13
rrl 1475881 n.2224T>G non_coding_transcript_exon_variant 0.13
rrl 1475882 n.2225C>G non_coding_transcript_exon_variant 0.13
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.13
rrl 1475895 n.2238C>G non_coding_transcript_exon_variant 0.13
rrl 1475897 n.2240T>G non_coding_transcript_exon_variant 0.13
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.13
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.13
rrl 1475914 n.2257C>T non_coding_transcript_exon_variant 0.14
rrl 1475920 n.2263G>C non_coding_transcript_exon_variant 0.14
rrl 1475924 n.2267A>G non_coding_transcript_exon_variant 0.13
rrl 1475933 n.2276C>G non_coding_transcript_exon_variant 0.14
rrl 1475939 n.2282G>C non_coding_transcript_exon_variant 0.15
rrl 1475944 n.2287G>A non_coding_transcript_exon_variant 0.15
rrl 1475947 n.2290G>A non_coding_transcript_exon_variant 0.15
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.13
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.11
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.11
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.11
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.12
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.12
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.12
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.14
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.14
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.14
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.14
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.14
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.16
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.15
rrl 1476353 n.2696G>A non_coding_transcript_exon_variant 0.18
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.19
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.23
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.23
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.21
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.25
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.24
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.24
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.18
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.14
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.11
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 2169998 c.615T>A synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.98
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243209 c.-23_-22delCG upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338563 c.-42G>T upstream_gene_variant 1.0
whiB6 4338593 c.-73delT upstream_gene_variant 1.0
whiB6 4338596 c.-75G>C upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0