TB-Profiler result

Run: SRR6046604
Summary

Run ID: SRR6046604

Sample name:

Date: 04-04-2023 12:19:53

Number of reads: 185294

Percentage reads mapped: 31.01

Strain: lineage2.2.1

Drug-resistance: Sensitive

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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
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.11
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.1
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
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 7559 c.258G>A synonymous_variant 0.25
gyrA 7571 c.270G>C synonymous_variant 0.25
gyrA 7574 c.273G>C synonymous_variant 0.25
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7587 c.286C>T synonymous_variant 0.33
gyrA 7595 c.294C>T synonymous_variant 0.33
gyrA 7601 c.300C>G synonymous_variant 0.33
gyrA 7619 c.318C>T synonymous_variant 0.25
gyrA 7706 c.405C>A synonymous_variant 0.33
gyrA 7710 c.409T>C synonymous_variant 0.33
gyrA 7715 c.414G>C synonymous_variant 0.33
gyrA 7721 c.420G>A synonymous_variant 0.33
gyrA 7728 c.427_429delAGGinsCGT synonymous_variant 0.33
gyrA 7760 c.459C>T synonymous_variant 0.33
gyrA 7763 c.462T>C synonymous_variant 0.33
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 619848 c.-43C>T upstream_gene_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761219 c.1413G>C synonymous_variant 1.0
rpoB 761234 c.1428G>C synonymous_variant 1.0
rpoB 761249 c.1443A>G synonymous_variant 1.0
rpoB 761255 c.1449T>G synonymous_variant 1.0
rpoB 761258 c.1452G>A synonymous_variant 1.0
rpoB 761261 c.1455G>C synonymous_variant 1.0
rpoB 761264 c.1458C>G synonymous_variant 1.0
rpoB 761273 c.1467T>C synonymous_variant 1.0
rpoC 762917 c.-453C>T upstream_gene_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763468 c.99G>C synonymous_variant 0.5
rpoC 763486 c.117T>C synonymous_variant 0.33
rpoC 763492 c.123G>C synonymous_variant 0.33
rpoC 763733 p.Pro122Ala missense_variant 0.25
rpoC 765058 c.1689C>T synonymous_variant 1.0
rpoC 765782 p.Ser805Pro missense_variant 0.5
rpoC 766645 p.Glu1092Asp missense_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 0.5
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.8
embR 1416266 p.Val361Ala missense_variant 0.33
embR 1416892 p.Asp152Glu missense_variant 0.14
embR 1417148 p.Gly67Asp missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471755 n.-91C>A upstream_gene_variant 1.0
rrs 1472606 n.761C>T non_coding_transcript_exon_variant 1.0
rrs 1472645 n.800G>A non_coding_transcript_exon_variant 1.0
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 1.0
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 1.0
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 1.0
fabG1 1673309 c.-131G>A upstream_gene_variant 0.5
rpsA 1833743 c.202C>T synonymous_variant 0.5
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834346 p.Arg269Cys missense_variant 0.5
tlyA 1917792 c.-148G>C upstream_gene_variant 0.5
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155190 p.Thr308Ala missense_variant 0.25
katG 2155926 p.Phe62Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168818 p.Gly599Ser missense_variant 0.5
PPE35 2170385 c.228G>T synonymous_variant 0.33
PPE35 2170392 p.Gly74Ala missense_variant 0.33
PPE35 2170400 c.213G>C synonymous_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289758 c.-517G>A upstream_gene_variant 0.33
kasA 2519006 p.Ala298Ser missense_variant 1.0
kasA 2519128 c.1014G>C synonymous_variant 0.5
kasA 2519131 c.1017G>C synonymous_variant 0.5
kasA 2519140 c.1026G>C synonymous_variant 0.5
kasA 2519143 c.1029G>C synonymous_variant 0.5
eis 2714825 p.Glu170* stop_gained 0.33
eis 2714929 p.Thr135Asn missense_variant 0.5
pepQ 2860344 p.Ser25Arg missense_variant 0.33
ribD 2986791 c.-48G>T upstream_gene_variant 0.2
ribD 2986824 c.-15G>T upstream_gene_variant 0.33
ribD 2987121 p.Gly95Cys missense_variant 0.5
ribD 2987195 c.357C>A synonymous_variant 0.25
ribD 2987278 p.Ala147Val missense_variant 0.5
Rv2752c 3064957 p.Ser412Asn missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338973 c.-145C>G upstream_gene_variant 0.5
Rv3083 3448404 c.-100C>T upstream_gene_variant 0.4
Rv3083 3449631 c.1128G>T synonymous_variant 1.0
whiB7 3568492 p.Trp63Leu missense_variant 0.5
Rv3236c 3612005 p.Arg371His missense_variant 1.0
Rv3236c 3613284 c.-168G>A upstream_gene_variant 0.25
rpoA 3877907 p.Ser201Ala missense_variant 1.0
embC 4240123 c.261C>T synonymous_variant 0.33
embC 4240500 p.Ser213Ile missense_variant 0.4
embC 4240590 p.Ala243Val missense_variant 0.5
embC 4240992 p.Ala377Val missense_variant 0.5
embC 4242371 p.Ala837Thr missense_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243416 p.Leu62Met missense_variant 1.0
embA 4244603 c.1371G>A synonymous_variant 0.5
embA 4244712 p.Ala494Ser missense_variant 0.2
embB 4247216 p.Ala235Ser missense_variant 0.22
embB 4249214 p.Glu901* stop_gained 0.5
embB 4249334 p.Ala941Thr missense_variant 0.4
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethR 4326567 c.-982G>T upstream_gene_variant 0.33
ethA 4328064 c.-591G>A upstream_gene_variant 0.5
whiB6 4338371 p.Thr51Pro missense_variant 0.5
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.8