TB-Profiler result

Run: SRR16058205
Summary

Run ID: SRR16058205

Sample name:

Date: 03-04-2023 15:31:43

Number of reads: 980697

Percentage reads mapped: 96.51

Strain: lineage2.2.1

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 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
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.11 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 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 620317 p.Val143Phe missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
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
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.93
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.14
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.12
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.18
rrl 1474584 n.927C>T non_coding_transcript_exon_variant 0.12
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.16
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.17
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.15
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.14
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.14
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.14
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 0.16
rrl 1474674 n.1017A>C non_coding_transcript_exon_variant 0.16
rrl 1474675 n.1018C>A non_coding_transcript_exon_variant 0.16
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.16
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.16
rrl 1474694 n.1037C>T non_coding_transcript_exon_variant 0.15
rrl 1474734 n.1077G>A non_coding_transcript_exon_variant 0.11
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.1
rrl 1474751 n.1094G>A non_coding_transcript_exon_variant 0.1
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.11
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.1
rrl 1474783 n.1126G>A non_coding_transcript_exon_variant 0.1
rrl 1475709 n.2052T>C non_coding_transcript_exon_variant 0.11
rrl 1476083 n.2426T>A non_coding_transcript_exon_variant 0.18
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.12
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.11
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.1
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.13
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.1
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.14
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.13
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.12
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.12
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.12
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.12
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.15
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290039 c.-798C>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449116 p.Ala205Thr missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474814 c.810delG frameshift_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly 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