TB-Profiler result

Run: SRR6369875
Summary

Run ID: SRR6369875

Sample name:

Date: 04-04-2023 13:41:42

Number of reads: 1013068

Percentage reads mapped: 98.68

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.Asp94Gly missense_variant 0.87 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.23 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.13 streptomycin
pncA 2289054 p.Asp63Gly missense_variant 0.17 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 0.35 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
gyrB 5834 p.Phe199Val missense_variant 0.29
gyrB 6416 p.Thr393Pro missense_variant 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8677 p.Glu459Ala missense_variant 0.25
gyrA 9025 p.Arg575Leu missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491377 p.Gly199Cys missense_variant 0.17
fgd1 491489 p.Asp236Ala missense_variant 0.22
fgd1 491542 c.760T>C synonymous_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.25
mshA 576123 p.Leu259Arg missense_variant 0.23
ccsA 619976 p.Leu29Arg missense_variant 0.18
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763087 p.Val1094Gly missense_variant 0.17
rpoC 763710 p.Leu114Arg missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775975 p.Leu836Met missense_variant 0.22
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777745 p.Gly246Ser missense_variant 0.93
mmpR5 779009 p.Val7Gly missense_variant 0.33
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303670 p.Asp247Ala missense_variant 0.2
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1417025 p.Asn108Ile missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.13
rrl 1473922 n.265A>C non_coding_transcript_exon_variant 1.0
rrl 1474896 n.1239A>T non_coding_transcript_exon_variant 0.38
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.13
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.15
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.17
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.18
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.17
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.17
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.15
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.15
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.15
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.15
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.17
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.18
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.17
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.17
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.2
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.2
rpsA 1833810 p.Val90Ala missense_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 2167905 p.Ile903Ser missense_variant 0.29
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168133 p.Asp827Ala missense_variant 0.25
PPE35 2168297 c.2315delC frameshift_variant 0.22
PPE35 2168463 p.Pro717Leu missense_variant 0.18
PPE35 2169122 c.1491C>G synonymous_variant 0.17
PPE35 2169144 p.Val490Glu missense_variant 0.2
Rv1979c 2223024 c.141G>T synonymous_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223320 c.-156T>G upstream_gene_variant 0.33
Rv2752c 3064566 c.1626G>C synonymous_variant 0.43
Rv2752c 3065377 p.Val272Asp missense_variant 0.2
Rv2752c 3065721 c.471G>T synonymous_variant 0.2
Rv2752c 3066024 c.168T>C synonymous_variant 0.18
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
fbiA 3640453 c.-90C>G upstream_gene_variant 0.2
rpoA 3878490 c.18C>G synonymous_variant 0.29
clpC1 4039832 c.873C>T synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244508 p.Leu426Val missense_variant 0.29
embB 4247913 p.Val467Gly missense_variant 0.21
embB 4247976 p.Val488Gly missense_variant 0.25
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267805 p.Phe344Leu missense_variant 0.15
aftB 4268826 p.Val4Gly missense_variant 0.38
ethA 4326098 p.Gln459Pro missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407560 p.Ser215Ala missense_variant 0.33
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0