TB-Profiler result

Run: ERR5864556
Summary

Run ID: ERR5864556

Sample name:

Date: 01-04-2023 23:25:33

Number of reads: 1468429

Percentage reads mapped: 74.73

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 0.93 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Trp missense_variant 0.93 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289208 p.Asp12Asn missense_variant 1.0 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin
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 7558 p.Pro86Gln missense_variant 0.11
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491174 p.Arg131Gln missense_variant 0.24
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 761505 p.Ser567Thr missense_variant 0.15
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 1304373 p.His481Gln missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.19
rrs 1472107 n.262A>G non_coding_transcript_exon_variant 0.12
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.19
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.11
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.11
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.11
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.11
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.14
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.22
rrs 1472522 n.677T>G non_coding_transcript_exon_variant 0.11
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.2
rrs 1472571 n.726G>T non_coding_transcript_exon_variant 0.22
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.19
rrs 1472582 n.737G>T non_coding_transcript_exon_variant 0.19
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.19
rrs 1472585 n.740A>C non_coding_transcript_exon_variant 0.19
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.17
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.13
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.16
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.13
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.11
rrl 1474017 n.360A>G non_coding_transcript_exon_variant 0.2
rrl 1474140 n.483C>A non_coding_transcript_exon_variant 0.18
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.12
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.11
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.12
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.14
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.28
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.21
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.21
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.21
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.19
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.14
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.14
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.13
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.13
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.17
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.21
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.11
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.15
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.16
rrl 1475978 n.2321C>T non_coding_transcript_exon_variant 0.11
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.25
rrl 1475991 n.2334T>A non_coding_transcript_exon_variant 0.12
rrl 1475993 n.2336C>T non_coding_transcript_exon_variant 0.19
rrl 1475996 n.2339T>G non_coding_transcript_exon_variant 0.13
rrl 1476031 n.2374C>T non_coding_transcript_exon_variant 0.2
rrl 1476035 n.2378G>C non_coding_transcript_exon_variant 0.18
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.12
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.12
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.12
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.13
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.12
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.14
rrl 1476251 n.2594T>A non_coding_transcript_exon_variant 0.13
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.13
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.13
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.14
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.23
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.18
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.22
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.25
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.38
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.29
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.31
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.27
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.23
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.53
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.43
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.12
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.12
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.15
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.14
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.14
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.29
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.13
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 2169016 p.Thr533Ala missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.45
PPE35 2170053 p.Thr187Ser missense_variant 0.42
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518506 p.Ala131Glu missense_variant 0.12
folC 2746747 c.852G>C synonymous_variant 1.0
Rv2752c 3065155 c.1036delG frameshift_variant 0.96
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
rpoA 3878567 c.-60C>G upstream_gene_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243960 p.Arg243Leu missense_variant 0.12
embB 4246548 p.Pro12Gln missense_variant 0.12
embB 4246555 c.42G>C synonymous_variant 0.13
embB 4246556 p.Ala15Pro missense_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4327065 p.Cys137Arg 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