TB-Profiler result

Run: SRR11972248
Summary

Run ID: SRR11972248

Sample name:

Date: 03-04-2023 05:33:27

Number of reads: 293848

Percentage reads mapped: 99.37

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 0.99
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
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 7315 p.Thr5Met missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8657 c.1356C>A synonymous_variant 0.2
gyrA 8699 c.1398A>G synonymous_variant 0.25
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9702 p.Val801Ile missense_variant 0.22
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575340 c.-8C>T upstream_gene_variant 0.22
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576359 p.Thr338Ala missense_variant 0.18
ccsA 620015 p.Arg42His missense_variant 0.22
ccsA 620439 c.553delG frameshift_variant 0.17
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760154 c.348C>T synonymous_variant 0.4
rpoB 760166 c.360C>T synonymous_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764704 c.1335G>A synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775834 p.Ala883Thr missense_variant 0.17
mmpL5 775994 c.2487C>A synonymous_variant 0.33
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776621 c.1860G>A synonymous_variant 0.14
mmpL5 777318 p.Arg388His missense_variant 0.25
mmpL5 778831 c.-351G>T upstream_gene_variant 0.18
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801154 p.Gly116Cys missense_variant 0.25
fbiC 1303396 p.Arg156Gly missense_variant 0.15
fbiC 1304516 p.Ala529Val missense_variant 0.17
Rv1258c 1406565 p.Gln259Arg missense_variant 0.13
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416745 c.603C>T synonymous_variant 0.15
embR 1417426 c.-79T>C upstream_gene_variant 0.12
atpE 1460935 c.-110T>C upstream_gene_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472784 n.939A>G non_coding_transcript_exon_variant 0.17
rrs 1472882 n.1037A>T non_coding_transcript_exon_variant 0.12
rrl 1473619 n.-39G>A upstream_gene_variant 0.13
rrl 1473899 n.242A>G non_coding_transcript_exon_variant 0.17
rrl 1474553 n.896T>C non_coding_transcript_exon_variant 1.0
rrl 1475339 n.1682T>A non_coding_transcript_exon_variant 0.14
fabG1 1673537 p.Gln33Arg missense_variant 0.2
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102594 p.Arg150His missense_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168140 p.Ala825Thr missense_variant 0.13
PPE35 2169503 c.1109delG frameshift_variant 0.14
PPE35 2169652 p.Leu321Ile missense_variant 0.22
PPE35 2169797 c.816G>T synonymous_variant 0.17
Rv1979c 2221961 p.Val402Leu missense_variant 0.12
Rv1979c 2222842 c.322delG frameshift_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289660 c.-419G>A upstream_gene_variant 0.22
kasA 2518088 c.-27T>C upstream_gene_variant 0.29
kasA 2518744 c.630C>T synonymous_variant 0.15
kasA 2518919 p.Gly269Ser missense_variant 0.2
eis 2714846 p.Val163Ile missense_variant 1.0
ribD 2986729 c.-110G>A upstream_gene_variant 0.25
Rv2752c 3065074 p.Ser373Phe missense_variant 0.22
Rv2752c 3066053 p.Val47Met missense_variant 0.18
Rv2752c 3066069 p.Leu41Phe missense_variant 0.29
thyA 3074438 p.Leu12Phe missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339471 c.354G>A synonymous_variant 0.25
Rv3083 3448622 p.Arg40His missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612360 p.Gly253Arg missense_variant 0.25
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3840824 c.597C>T synonymous_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.25
rpoA 3877611 p.Ile299Met missense_variant 0.13
rpoA 3878039 p.Ala157Ser missense_variant 0.18
clpC1 4039441 p.Arg422Ser missense_variant 0.15
clpC1 4039473 p.Arg411Pro missense_variant 0.2
embC 4240242 p.Asn127Ser missense_variant 0.11
embC 4241125 c.1263G>A synonymous_variant 0.18
embC 4242492 p.Arg877Gln missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242944 p.Asn1028Asp missense_variant 0.1
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4248115 c.1602C>T synonymous_variant 0.98
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4269270 c.-434G>A upstream_gene_variant 0.33
ethA 4327142 p.Thr111Ile missense_variant 0.2
whiB6 4338278 p.Pro82Ser missense_variant 0.14
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