TB-Profiler result

Run: SRR6257052
Summary

Run ID: SRR6257052

Sample name:

Date: 04-04-2023 13:24:29

Number of reads: 475918

Percentage reads mapped: 99.57

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 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288719 p.Met175Val missense_variant 0.12 pyrazinamide
pncA 2288928 p.Gly105Asp missense_variant 1.0 pyrazinamide
embB 4247399 p.Asn296His missense_variant 1.0 ethambutol
ethA 4327363 c.110delA 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
gyrB 5990 p.Phe251Leu missense_variant 0.18
gyrB 7082 p.Glu615Lys missense_variant 0.11
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
mshA 576662 p.Ala439Pro missense_variant 0.17
mshA 576695 p.Ala450Thr missense_variant 0.18
ccsA 619787 c.-104T>A upstream_gene_variant 0.11
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 763026 p.Gly1074Cys missense_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 767243 p.Tyr1292Asn missense_variant 0.11
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 776424 p.Asp686Gly missense_variant 0.13
mmpL5 778312 p.Gly57Arg missense_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302822 c.-109T>G upstream_gene_variant 0.13
fbiC 1304887 p.Leu653Met missense_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673406 c.-796C>T upstream_gene_variant 1.0
fabG1 1673810 p.Ser124Leu missense_variant 0.12
rpsA 1833623 p.Lys28Glu missense_variant 0.14
rpsA 1834007 p.Arg156Cys missense_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834249 p.His236Gln missense_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918417 c.478T>C synonymous_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155938 p.Met58Ile missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168448 c.2164delC frameshift_variant 0.11
PPE35 2168863 p.Leu584Met missense_variant 0.15
PPE35 2170511 c.102G>A synonymous_variant 0.12
Rv1979c 2223034 p.Gly44Val missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747249 p.Pro117Leu missense_variant 0.15
thyA 3074567 c.-96C>A upstream_gene_variant 0.12
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087311 c.494dupG frameshift_variant 1.0
fbiD 3339520 p.His135Asp missense_variant 0.17
Rv3083 3449304 c.801A>G synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641161 p.Asp207Tyr missense_variant 0.17
alr 3840464 p.Phe319Leu missense_variant 0.13
alr 3840934 p.Asn163Asp missense_variant 0.1
rpoA 3877850 p.Gly220Ser missense_variant 0.12
rpoA 3877949 p.Thr187Ala missense_variant 1.0
embC 4239677 c.-186C>A upstream_gene_variant 0.11
embC 4239951 p.Arg30Leu missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.87
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244058 c.827delA frameshift_variant 0.12
embA 4244748 p.Thr506Ala missense_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268218 p.Trp207Arg missense_variant 0.17
ubiA 4269298 p.Ile179Thr missense_variant 1.0
ubiA 4269323 p.Pro171Ser missense_variant 0.12
ethA 4328271 c.-798A>G upstream_gene_variant 0.12
ethA 4328416 c.-943G>T upstream_gene_variant 0.12
whiB6 4338371 p.Thr51Pro 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