TB-Profiler result

Run: ERR4827448
Summary

Run ID: ERR4827448

Sample name:

Date: 01-04-2023 18:03:23

Number of reads: 1744550

Percentage reads mapped: 99.37

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 7570 p.Ala90Val missense_variant 0.53 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7572 p.Ser91Pro missense_variant 0.47 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289066 p.Ser59Phe missense_variant 0.54 pyrazinamide
pncA 2289207 p.Asp12Ala missense_variant 0.5 pyrazinamide
eis 2715346 c.-14C>T upstream_gene_variant 1.0 kanamycin, amikacin
embB 4247431 p.Met306Ile 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 575210 c.-137delG upstream_gene_variant 0.17
mshA 575774 p.His143Asn missense_variant 0.14
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.27
mshA 576111 p.Ala255Gly missense_variant 0.2
mshA 576228 p.Arg294His missense_variant 0.17
mshA 576388 c.1041G>A synonymous_variant 0.2
mshA 576616 c.1269G>A synonymous_variant 0.17
ccsA 619998 c.108C>T synonymous_variant 0.18
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760566 p.Ser254Pro missense_variant 0.13
rpoB 762310 p.His835Arg missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766290 p.Val974Ala missense_variant 0.12
rpoC 766536 p.Glu1056Val missense_variant 0.13
rpoC 766637 p.Lys1090Gln missense_variant 0.2
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
mmpL5 777535 p.Thr316Ala missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304334 p.Ser468Arg missense_variant 0.11
fbiC 1304442 c.1512T>C synonymous_variant 0.11
fbiC 1304446 c.1516_1517insT frameshift_variant 0.13
Rv1258c 1406303 c.1038C>A synonymous_variant 0.13
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102248 c.795C>T synonymous_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167955 c.2658A>C synonymous_variant 0.21
PPE35 2169602 c.1011C>A synonymous_variant 0.17
PPE35 2169732 p.Asn294Ser missense_variant 0.17
PPE35 2169902 c.711G>C synonymous_variant 0.14
PPE35 2170048 p.Leu189Val missense_variant 0.43
PPE35 2170053 p.Thr187Ser missense_variant 0.46
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518673 p.Met187Val missense_variant 0.12
kasA 2519140 c.1026G>C synonymous_variant 0.17
kasA 2519143 c.1029G>C synonymous_variant 0.17
eis 2715227 p.Trp36Arg missense_variant 0.48
eis 2715330 c.3G>A synonymous_variant 0.57
pepQ 2859700 p.Gly240Asp missense_variant 0.29
Rv2752c 3064731 p.Leu487Phe missense_variant 1.0
Rv2752c 3064943 p.Gln417* stop_gained 0.42
Rv2752c 3065749 p.His148Arg missense_variant 0.51
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
alr 3841546 c.-126C>A upstream_gene_variant 0.25
clpC1 4038303 p.Thr801Asn missense_variant 0.12
clpC1 4038389 c.2315delC frameshift_variant 0.13
clpC1 4039645 p.His354Asp missense_variant 0.2
clpC1 4040144 c.561G>C synonymous_variant 0.18
embA 4242379 c.-854G>T upstream_gene_variant 0.23
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245474 p.Gly748Arg missense_variant 0.14
embA 4245844 p.Val871Asp missense_variant 0.12
embA 4245846 p.Ser872Thr missense_variant 0.12
embA 4245848 c.2616_2617insACCACCA frameshift_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.16
embB 4246548 p.Pro12Gln missense_variant 0.41
embB 4246555 c.42G>C synonymous_variant 0.53
embB 4246556 p.Ala15Pro missense_variant 0.53
embB 4246563 p.Leu17Trp missense_variant 0.33
embB 4246567 c.54G>T synonymous_variant 0.5
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268918 c.-82G>A upstream_gene_variant 1.0
aftB 4269090 c.-254C>T upstream_gene_variant 0.13
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