TB-Profiler result

Run: SRR6257023

Summary

Run ID: SRR6257023

Sample name:

Date: 04-04-2023 13:23:21

Number of reads: 468816

Percentage reads mapped: 99.24

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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
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 5234 c.-6C>A upstream_gene_variant 0.12
gyrB 5434 c.195G>A synonymous_variant 0.12
gyrA 6460 c.-842G>T upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8131 p.Gln277Arg missense_variant 0.12
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
rpoB 760825 p.Val340Gly missense_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763582 p.Lys71Asn missense_variant 0.1
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775882 p.Asn867Asp missense_variant 0.1
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
fbiC 1303265 p.Gly112Asp missense_variant 0.22
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407475 c.-135G>A upstream_gene_variant 0.11
atpE 1461241 p.Ile66Thr missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473519 n.-139T>A upstream_gene_variant 0.2
rrl 1476122 n.2465A>G non_coding_transcript_exon_variant 0.15
inhA 1674117 c.-85C>T upstream_gene_variant 0.15
rpsA 1834171 c.630C>T synonymous_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101917 p.Phe376Leu missense_variant 0.11
ndh 2102196 p.Ser283Gly missense_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155511 p.Glu201Lys missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168116 p.Gly833Ser missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714547 p.Met262Ile missense_variant 0.11
ahpC 2726232 p.Gln14* stop_gained 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339724 p.Val203Leu missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474070 c.64T>C synonymous_variant 0.12
whiB7 3568581 c.99G>T synonymous_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3840521 c.900C>T synonymous_variant 0.13
alr 3841441 c.-22delG upstream_gene_variant 0.1
rpoA 3878634 c.-127C>A upstream_gene_variant 0.22
ddn 3987176 c.334delC frameshift_variant 0.12
embC 4240701 p.Val280Glu missense_variant 0.12
embC 4241303 p.Thr481Ala missense_variant 0.12
embC 4242047 p.Ser729Thr missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245934 p.Pro901Gln missense_variant 0.18
embB 4246660 c.147C>T synonymous_variant 0.12
embB 4249754 p.Gly1081Cys missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268276 c.561G>A synonymous_variant 0.14
aftB 4268431 p.Thr136Pro missense_variant 0.17
whiB6 4338298 p.Leu75Gln missense_variant 1.0
whiB6 4338563 c.-42G>T upstream_gene_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