TB-Profiler result

Run: SRR11972356
Summary

Run ID: SRR11972356

Sample name:

Date: 03-04-2023 05:38:23

Number of reads: 1270418

Percentage reads mapped: 99.1

Strain: lineage2.2.1.1

Drug-resistance: HR-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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
folC 2747141 p.Glu153Ala missense_variant 1.0 para-aminosalicylic_acid
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 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620652 c.762C>G synonymous_variant 0.15
rpoB 762513 p.Asp903His missense_variant 0.15
rpoB 762688 p.Gln961Arg missense_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766459 c.3090G>A synonymous_variant 0.12
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 777860 c.621C>T synonymous_variant 0.14
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
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.12
rrl 1474553 n.896T>C non_coding_transcript_exon_variant 0.93
inhA 1674616 p.Asn139Asp missense_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834703 p.Gly388Cys missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918521 c.582C>T synonymous_variant 0.22
katG 2153975 p.Ala713Thr missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155130 p.Trp328Arg missense_variant 0.1
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288976 p.Ala89Val missense_variant 0.14
eis 2714846 p.Val163Ile missense_variant 1.0
eis 2714993 p.Pro114Ala missense_variant 0.17
folC 2746455 c.1144C>T synonymous_variant 0.15
folC 2746757 p.Gly281Val missense_variant 0.12
folC 2747247 p.Ala118Thr missense_variant 0.12
ribD 2987090 c.252C>A synonymous_variant 0.12
Rv2752c 3066336 c.-146delG upstream_gene_variant 0.17
Rv2752c 3067010 c.-819A>T upstream_gene_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339087 c.-31C>T upstream_gene_variant 0.2
fbiD 3339561 c.444C>A synonymous_variant 0.15
Rv3083 3449697 c.1194G>A synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611985 p.Pro378Ser missense_variant 0.15
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641813 p.Leu93Phe missense_variant 0.12
fbiB 3642348 p.Pro272Thr missense_variant 0.2
fbiB 3642663 p.Val377Phe missense_variant 0.15
alr 3840898 c.522dupC frameshift_variant 0.18
clpC1 4039520 c.1185G>T synonymous_variant 0.14
clpC1 4039632 p.Ile358Asn missense_variant 0.15
embC 4240901 p.Pro347Ser missense_variant 0.18
embC 4241541 p.Thr560Ile missense_variant 0.12
embC 4241578 c.1716G>A synonymous_variant 0.12
embC 4241720 p.Thr620Ala missense_variant 0.15
embC 4242329 p.Glu823* stop_gained 0.29
embA 4242511 c.-722G>C upstream_gene_variant 0.33
embC 4242576 p.Gln905Leu missense_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242665 p.Ala935Ser missense_variant 0.22
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.5
embB 4246548 p.Pro12Gln missense_variant 0.38
embB 4246555 c.42G>C synonymous_variant 0.38
embB 4246556 p.Ala15Pro missense_variant 0.38
embB 4246754 p.Ala81Thr missense_variant 0.18
embB 4247524 c.1011G>A synonymous_variant 0.12
embB 4248115 c.1602C>T synonymous_variant 1.0
aftB 4267057 p.Ser594Pro missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326031 c.1443C>A synonymous_variant 0.11
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