TB-Profiler result

Run: SRR19428558

Summary

Run ID: SRR19428558

Sample name:

Date: 03-04-2023 21:40:12

Number of reads: 400039

Percentage reads mapped: 99.57

Strain: lineage3.1;lineage2.2.1

Drug-resistance: RR-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 0.11
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.16
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.23
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.09
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
rpoB 761155 p.Ser450Leu missense_variant 0.22 rifampicin
embB 4247431 p.Met306Ile missense_variant 0.13 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 7078 c.-224A>T upstream_gene_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8688 p.Ala463Ser missense_variant 0.32
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9485 c.2189delG frameshift_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 0.56
mshA 575870 p.His175Asp missense_variant 0.14
mshA 575907 p.Ala187Val missense_variant 0.42
mshA 576077 c.730C>T synonymous_variant 0.42
mshA 576329 p.Leu328Met missense_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 0.14
rpoB 759746 c.-61C>T upstream_gene_variant 0.25
rpoB 760608 c.802C>T synonymous_variant 0.12
rpoB 761489 c.1683G>A synonymous_variant 0.5
rpoC 762434 c.-936T>G upstream_gene_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 0.6
rpoC 763584 c.220_222delATC conservative_inframe_deletion 0.1
rpoC 763641 p.Arg91Leu missense_variant 0.11
rpoC 764244 p.Ala292Val missense_variant 0.11
rpoC 765523 c.2154C>T synonymous_variant 0.11
rpoC 767046 p.Phe1226Ser missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.62
mmpL5 776304 p.Pro726Gln missense_variant 0.11
mmpL5 778305 p.Ile59Thr missense_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781441 c.-119C>T upstream_gene_variant 0.12
rpsL 781453 c.-107C>A upstream_gene_variant 0.12
rplC 801251 p.Pro148Leu missense_variant 0.11
rplC 801264 c.456C>G synonymous_variant 0.11
fbiC 1304163 c.1233G>T synonymous_variant 0.13
fbiC 1305430 p.Val834Ile missense_variant 0.17
embR 1416636 c.710_711delAC frameshift_variant 0.17
embR 1417511 c.-166_-165delAC upstream_gene_variant 0.1
atpE 1461210 p.Thr56Ser missense_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471898 n.53A>T non_coding_transcript_exon_variant 0.11
rrl 1474489 n.832T>C non_coding_transcript_exon_variant 0.12
rrl 1475259 n.1602T>G non_coding_transcript_exon_variant 0.56
inhA 1673514 c.-688G>T upstream_gene_variant 0.17
fabG1 1673803 p.Arg122Trp missense_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103118 c.-76T>A upstream_gene_variant 0.13
katG 2154357 c.1755C>T synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 0.54
PPE35 2167926 p.Leu896Ser missense_variant 0.62
PPE35 2168232 p.Ile794Asn missense_variant 0.13
PPE35 2170461 p.Gly51Glu missense_variant 0.33
PPE35 2170783 c.-171A>G upstream_gene_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289351 c.-110C>A upstream_gene_variant 0.12
pncA 2289365 c.-125delC upstream_gene_variant 0.24
pncA 2290026 c.-785C>G upstream_gene_variant 0.11
pncA 2290027 c.-786G>A upstream_gene_variant 0.11
kasA 2518584 c.471_472dupGC frameshift_variant 0.13
kasA 2518618 c.505delT frameshift_variant 0.14
eis 2714227 p.Leu369Ser missense_variant 0.17
eis 2714307 c.1025dupC frameshift_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 0.17
pepQ 2860070 p.Lys117Glu missense_variant 0.13
pepQ 2860154 p.Glu89Gln missense_variant 0.2
pepQ 2860419 c.-1C>G upstream_gene_variant 0.25
pepQ 2860451 c.-33G>A upstream_gene_variant 0.22
ribD 2987339 c.501C>A synonymous_variant 0.15
Rv2752c 3064632 c.1560C>T synonymous_variant 0.12
Rv2752c 3064776 c.1416T>C synonymous_variant 0.13
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.42
Rv2752c 3067176 c.-986delG upstream_gene_variant 0.12
thyA 3074110 p.Thr121Ile missense_variant 0.12
thyA 3074312 p.Ser54Thr missense_variant 0.11
ald 3086742 c.-78A>C upstream_gene_variant 0.39
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086977 p.Ala53Val missense_variant 0.17
Rv3083 3448429 c.-75C>A upstream_gene_variant 0.13
Rv3083 3449222 p.Tyr240Phe missense_variant 0.15
Rv3083 3449346 c.843G>A synonymous_variant 0.22
Rv3083 3449982 c.1479G>A synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474180 c.174C>A synonymous_variant 0.12
fprA 3475274 p.Trp423Leu missense_variant 0.12
rpoA 3877985 p.Thr175Ala missense_variant 0.12
clpC1 4039344 c.1360delG frameshift_variant 0.1
clpC1 4039753 p.Gln318Lys missense_variant 0.12
clpC1 4040099 p.Gln202His missense_variant 0.12
embC 4240172 p.Val104Met missense_variant 0.44
embC 4241042 p.Asn394Asp missense_variant 0.13
embC 4242075 p.Arg738Gln missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243236 p.Pro2Thr missense_variant 0.18
embA 4243449 p.Ser73Pro missense_variant 0.11
embA 4243460 c.228C>T synonymous_variant 0.11
embA 4245798 p.Trp856Arg missense_variant 0.17
embA 4246200 p.Gln990Glu missense_variant 0.12
embA 4246291 c.3060delA frameshift_variant 0.11
embB 4246635 p.Ser41Leu missense_variant 0.22
embB 4247106 p.Pro198Arg missense_variant 0.1
embB 4247161 c.648G>C synonymous_variant 0.15
embB 4249346 p.Ala945Ser missense_variant 0.11
embB 4249694 c.3185delG frameshift_variant 0.25
aftB 4267647 p.Asp397Gly missense_variant 0.33
aftB 4268167 p.Tyr224His missense_variant 0.14
ethR 4328129 p.Val194Ala missense_variant 0.14
whiB6 4338367 p.Leu52Gln missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407562 p.Gly214Val missense_variant 0.12
gid 4407588 c.615A>G synonymous_variant 0.29
gid 4407622 p.Asn194Ser missense_variant 0.14
gid 4407927 p.Glu92Asp missense_variant 0.19
gid 4408265 c.-63T>C upstream_gene_variant 0.12