TB-Profiler result

Run: SRR6045474
Summary

Run ID: SRR6045474

Sample name:

Date: 04-04-2023 12:00:03

Number of reads: 349059

Percentage reads mapped: 99.13

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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, 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 6932 p.Gln565Lys missense_variant 0.17
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 620748 c.858T>G synonymous_variant 0.57
rpoB 760505 c.702_703delGC frameshift_variant 0.29
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
mmpL5 777928 p.Tyr185His missense_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303091 p.Glu54Val missense_variant 0.18
fbiC 1303094 p.Leu55Pro missense_variant 0.18
fbiC 1305267 c.2337C>A synonymous_variant 0.2
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473827 n.170G>T non_coding_transcript_exon_variant 1.0
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.4
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.4
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.33
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.33
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.29
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.29
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.25
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.22
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.22
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.22
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.29
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.29
rpsA 1833491 c.-50delG upstream_gene_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101802 p.Leu414Gln missense_variant 0.29
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155401 c.711C>A synonymous_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169198 p.Val472Gly missense_variant 1.0
PPE35 2169312 p.Thr434Lys missense_variant 0.22
PPE35 2169895 p.Gly240Ser missense_variant 0.18
PPE35 2170066 p.Ala183Thr missense_variant 0.25
PPE35 2170349 p.Thr88Ala missense_variant 0.29
PPE35 2170357 p.Ala86Thr missense_variant 0.25
PPE35 2170371 p.Thr81Val missense_variant 0.25
PPE35 2170385 c.228G>T synonymous_variant 0.22
PPE35 2170392 p.Gly74Ala missense_variant 0.22
PPE35 2170400 c.213G>C synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290122 c.-882dupG upstream_gene_variant 0.25
eis 2714413 p.Ala307Gly missense_variant 0.33
folC 2747320 c.279C>T synonymous_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475064 p.Asn353Ile missense_variant 0.15
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612835 c.282T>G synonymous_variant 0.2
panD 4044463 c.-185_-183delTAC upstream_gene_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244054 c.822C>T synonymous_variant 0.17
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4246548 p.Pro12Gln missense_variant 0.33
embB 4246555 c.42G>C synonymous_variant 0.29
embB 4246556 p.Ala15Pro missense_variant 0.29
embB 4246563 p.Leu17Trp missense_variant 0.33
embB 4246567 c.54G>T synonymous_variant 0.33
embB 4247531 p.Met340Val missense_variant 0.2
embB 4249732 c.3219C>T synonymous_variant 0.2
embB 4249757 p.Thr1082Ala missense_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338375 c.147C>G synonymous_variant 0.22
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