TB-Profiler result

Run: ERR1194811
Summary

Run ID: ERR1194811

Sample name:

Date: 31-03-2023 12:34:27

Number of reads: 683873

Percentage reads mapped: 99.13

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
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 5990 p.Phe251Leu missense_variant 0.29
gyrB 7067 p.Tyr610Asp missense_variant 0.18
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 490884 c.102C>T synonymous_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576231 p.Ile295Ser missense_variant 0.2
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761609 p.Met601Ile missense_variant 0.22
rpoB 762577 p.Gln924Leu missense_variant 0.29
rpoB 762628 p.Asp941Ala missense_variant 0.38
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763187 c.-183C>T upstream_gene_variant 0.33
rpoB 763295 p.Asn1163Lys missense_variant 0.15
rpoC 763383 p.Asn5Ile missense_variant 0.18
rpoC 763608 p.Val80Gly missense_variant 0.29
rpoC 766100 p.Ile911Leu missense_variant 0.18
rpoC 766643 p.Glu1092Tyr missense_variant 0.29
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 776546 p.Met645Ile missense_variant 0.17
mmpL5 779007 c.-527C>G upstream_gene_variant 0.2
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303699 p.Thr257Ser missense_variant 0.33
fbiC 1304067 c.1137G>T synonymous_variant 0.29
fbiC 1305096 c.2166T>C synonymous_variant 0.11
Rv1258c 1406106 p.Asp412Ala missense_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407039 p.Val101Gly missense_variant 0.33
embR 1416482 p.Val289Glu missense_variant 0.12
atpE 1460880 c.-165A>G upstream_gene_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473396 n.-262A>T upstream_gene_variant 0.91
inhA 1674763 p.Leu188Val missense_variant 0.2
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102045 c.997delG frameshift_variant 0.15
katG 2154639 c.1473C>T synonymous_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167745 p.Thr956Arg missense_variant 0.2
PPE35 2167814 c.2799C>T synonymous_variant 0.18
PPE35 2167847 c.2766A>T synonymous_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168476 p.Pro713Thr missense_variant 0.33
PPE35 2169902 p.Leu237Phe missense_variant 0.29
PPE35 2169910 p.Asn235Tyr missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859430 p.Leu330* stop_gained 0.33
pepQ 2859925 p.Pro165Leu missense_variant 0.18
ribD 2986837 c.-2T>A upstream_gene_variant 0.22
Rv2752c 3065500 p.Gly231Val missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448947 c.444T>A synonymous_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612510 p.Gly203Cys missense_variant 0.4
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612860 p.Leu86Gln missense_variant 0.33
Rv3236c 3613010 p.Tyr36Phe missense_variant 0.25
fbiB 3640827 c.-708T>C upstream_gene_variant 0.11
alr 3840873 p.Met183Lys missense_variant 0.25
alr 3841503 c.-83G>A upstream_gene_variant 0.15
rpoA 3878490 c.18C>G synonymous_variant 0.33
clpC1 4039829 p.Leu292Ile missense_variant 0.29
embC 4240335 p.Thr158Ile missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243944 p.Thr238Pro missense_variant 0.18
embA 4244482 p.Leu417Arg missense_variant 0.2
embA 4244610 p.Ala460Ser missense_variant 0.22
embA 4245056 c.1824C>A synonymous_variant 0.15
embB 4246643 p.Thr44Pro missense_variant 0.33
aftB 4267224 p.Ile538Ser missense_variant 0.2
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
gid 4408050 p.Asn51Lys missense_variant 0.12