TB-Profiler result

Run: SRR18002906
Summary

Run ID: SRR18002906

Sample name:

Date: 03-04-2023 19:09:31

Number of reads: 4382935

Percentage reads mapped: 96.05

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 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.97 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.27 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.2 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.13 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289016 p.Thr76Pro missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326721 c.752dupG frameshift_variant 1.0 ethionamide, ethionamide
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 491286 c.504G>C synonymous_variant 1.0
fgd1 491315 p.Gly178Ala missense_variant 0.24
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.37
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764888 p.Leu507Val 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 1472102 n.257G>A non_coding_transcript_exon_variant 0.12
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.12
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.12
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.16
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.14
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.25
rrs 1472496 n.651T>A non_coding_transcript_exon_variant 0.25
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.23
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.14
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.14
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.14
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.14
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.27
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.12
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.32
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.12
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.11
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.41
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.35
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.12
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.3
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.23
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.2
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.17
rrs 1472674 n.829T>G non_coding_transcript_exon_variant 0.17
rrs 1472675 n.830T>A non_coding_transcript_exon_variant 0.16
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.16
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.15
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.16
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.16
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.11
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.14
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.13
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.2
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.17
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 0.17
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.18
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.14
rrs 1473305 n.1460G>T non_coding_transcript_exon_variant 0.16
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.15
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.19
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.24
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.11
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.11
rrl 1475288 n.1631G>A non_coding_transcript_exon_variant 0.11
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.26
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.24
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.25
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.25
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.25
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.24
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.22
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.21
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.19
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 0.16
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.16
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.16
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.13
rrl 1475978 n.2321C>T non_coding_transcript_exon_variant 0.13
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.12
rrl 1476001 n.2344T>C non_coding_transcript_exon_variant 0.12
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.1
rrl 1476034 n.2377C>G non_coding_transcript_exon_variant 0.1
rrl 1476045 n.2388G>T non_coding_transcript_exon_variant 0.12
rrl 1476047 n.2390G>T non_coding_transcript_exon_variant 0.12
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.12
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.17
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.14
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.14
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.14
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.16
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.16
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.2
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.27
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.29
rrl 1476253 n.2596A>G non_coding_transcript_exon_variant 0.3
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.31
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.3
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.31
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.28
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.27
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.27
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.27
rrl 1476299 n.2642C>G non_coding_transcript_exon_variant 0.27
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.27
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.27
rrl 1476308 n.2651G>C non_coding_transcript_exon_variant 0.27
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.27
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.26
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.26
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.14
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.12
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.21
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.14
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.15
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.12
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.16
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.15
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.15
rrl 1476481 n.2824T>C 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
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 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878576 c.-69T>G upstream_gene_variant 0.26
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 0.12
embB 4246548 p.Pro12Gln missense_variant 0.21
embB 4246555 c.42G>C synonymous_variant 0.21
embB 4246556 p.Ala15Pro missense_variant 0.21
embB 4246563 p.Leu17Trp missense_variant 0.24
embB 4246567 c.54G>T synonymous_variant 0.21
embB 4247028 p.Leu172Arg missense_variant 0.32
embB 4248200 p.Ile563Leu missense_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407912 c.291C>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0