TB-Profiler result

Run: SRR4037815
Summary

Run ID: SRR4037815

Sample name:

Date: 04-04-2023 07:41:29

Number of reads: 447368

Percentage reads mapped: 99.32

Strain: lineage2.2.1

Drug-resistance: Other

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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
ethA 4326026 c.1447delA frameshift_variant 0.22 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 5359 c.122dupG frameshift_variant 0.25
gyrB 5753 c.514C>A synonymous_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9056 c.1755C>A synonymous_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491152 p.Glu124Lys missense_variant 0.15
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
rpoB 760019 c.213G>T synonymous_variant 0.17
rpoB 760254 p.Asp150Tyr missense_variant 0.13
rpoB 760721 c.915C>A synonymous_variant 0.22
rpoB 760748 c.942C>A synonymous_variant 0.22
rpoB 761626 p.Arg607His missense_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763041 p.Leu1079Met missense_variant 0.29
rpoC 764299 p.Met310Ile missense_variant 0.22
rpoC 764407 p.Arg346Ser missense_variant 0.13
rpoC 765965 p.Arg866Ser missense_variant 0.2
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpR5 779452 p.Gly155Trp missense_variant 0.33
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781923 p.Glu122* stop_gained 0.23
fbiC 1303974 c.1044C>A synonymous_variant 0.22
fbiC 1305081 c.2151G>A synonymous_variant 0.25
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407233 p.Gln36His missense_variant 0.29
embR 1416932 p.Ser139* stop_gained 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472129 n.284G>T non_coding_transcript_exon_variant 0.12
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 0.22
rrs 1472706 n.861C>A non_coding_transcript_exon_variant 0.15
rrl 1474439 n.782A>G non_coding_transcript_exon_variant 0.29
rrl 1475150 n.1493C>T non_coding_transcript_exon_variant 0.25
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834736 p.Glu399Lys missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156366 c.-255G>T upstream_gene_variant 0.25
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168902 p.Pro571Thr missense_variant 0.12
PPE35 2169569 c.1044C>T synonymous_variant 0.12
PPE35 2169866 c.747G>C synonymous_variant 0.2
Rv1979c 2221842 c.1323G>T synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289549 c.-308G>A upstream_gene_variant 0.13
eis 2714138 c.1185_1194delCGTCCAGACC frameshift_variant 0.22
eis 2715230 p.Ala35Ser missense_variant 0.22
folC 2746665 p.Phe312Leu missense_variant 0.25
folC 2747161 c.438C>T synonymous_variant 0.33
Rv2752c 3065093 p.Gln367Lys missense_variant 0.13
Rv2752c 3066062 p.Asp44Tyr missense_variant 0.2
Rv2752c 3066142 p.Arg17Leu missense_variant 0.29
thyX 3067765 p.Leu61Ile missense_variant 0.17
thyA 3074272 p.Ser67Cys missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087374 c.555C>A synonymous_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568783 c.-104A>G upstream_gene_variant 0.22
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3840221 p.Arg400Ser missense_variant 0.22
alr 3840552 p.Gly290Val missense_variant 0.12
alr 3840785 c.636C>A synonymous_variant 0.17
clpC1 4039249 p.Glu486Lys missense_variant 0.29
clpC1 4040727 c.-24_-23insG upstream_gene_variant 0.22
embC 4241359 c.1497C>T synonymous_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244246 c.1014C>A synonymous_variant 0.17
embA 4244967 p.Gly579Trp missense_variant 0.2
embB 4245959 c.-555G>T upstream_gene_variant 0.33
embA 4246227 c.2997delT frameshift_variant 0.17
embB 4247210 p.Leu233Met missense_variant 0.29
embB 4247955 p.Pro481Gln missense_variant 0.17
embB 4247964 p.Ala484Asp missense_variant 0.14
embB 4248439 c.1926C>A synonymous_variant 0.17
embB 4248779 p.Glu756Lys missense_variant 0.18
embB 4249184 p.Gly891Trp missense_variant 0.29
aftB 4267531 p.Ala436Thr missense_variant 0.29
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4269102 c.-266C>T upstream_gene_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338666 c.-145G>T upstream_gene_variant 0.12
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0