TB-Profiler result

Run: SRR7646020
Summary

Run ID: SRR7646020

Sample name:

Date: 04-04-2023 20:03:39

Number of reads: 1286620

Percentage reads mapped: 99.58

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 0.91 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.96 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 2288767 p.Leu159Val missense_variant 1.0 pyrazinamide
embB 4247729 p.Gly406Ser missense_variant 1.0 ethambutol
ethA 4327363 c.110delA frameshift_variant 0.92 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 5616 p.Ser126Leu missense_variant 0.11
gyrB 5739 p.Thr167Met missense_variant 0.11
gyrB 7261 p.Asp674Glu missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9202 p.Lys634Met missense_variant 0.12
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 576281 c.934C>T synonymous_variant 0.25
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620657 c.769delC frameshift_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764501 p.Val378Met missense_variant 0.1
rpoC 764526 p.Arg386His missense_variant 0.11
rpoC 764532 p.Gly388Ala missense_variant 0.12
rpoC 764840 p.Ile491Val missense_variant 1.0
rpoC 764871 p.Ala501Val missense_variant 0.12
rpoC 765084 p.Arg572His missense_variant 0.15
rpoC 765934 c.2565C>T synonymous_variant 0.11
rpoC 766234 c.2867delG frameshift_variant 0.25
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 779133 c.-653G>T upstream_gene_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781578 c.19C>T synonymous_variant 0.11
rplC 801135 c.327C>T synonymous_variant 0.2
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407055 c.285delG frameshift_variant 0.2
embR 1416400 c.948C>T synonymous_variant 0.12
embR 1417386 c.-39T>C upstream_gene_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473463 n.-195C>T upstream_gene_variant 0.17
rrl 1474589 n.932T>A non_coding_transcript_exon_variant 0.14
inhA 1674042 c.-160G>A upstream_gene_variant 0.13
rpsA 1834100 p.Arg187Ser missense_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102024 c.1018delG frameshift_variant 0.15
ndh 2103230 c.-189delG upstream_gene_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156442 c.-331G>A upstream_gene_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168791 p.Pro608Ser missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860131 c.287delG frameshift_variant 0.1
ribD 2987469 c.635_636delGT frameshift_variant 0.14
Rv2752c 3065903 c.289C>A synonymous_variant 0.11
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448805 p.Gly101Asp missense_variant 1.0
Rv3083 3449267 p.Tyr255Cys missense_variant 0.1
fprA 3473970 c.-37_-36insA upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474244 p.Gly80Ser missense_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641181 c.-354G>A upstream_gene_variant 0.11
alr 3840353 c.1068T>C synonymous_variant 0.14
ddn 3986688 c.-156G>A upstream_gene_variant 0.13
clpC1 4039395 p.Ser437Leu missense_variant 0.25
embC 4240580 p.Leu240Ile missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242882 p.Pro1007Leu missense_variant 0.18
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244520 c.1292delC frameshift_variant 0.12
embA 4244820 p.Gly530Arg missense_variant 0.12
embB 4248626 c.2117delC frameshift_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267826 c.1011G>T synonymous_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