TB-Profiler result

Run: ERR11050164
Summary

Run ID: ERR11050164

Sample name:

Date: 02-04-2023 14:27:43

Number of reads: 525513

Percentage reads mapped: 99.23

Strain: lineage1.1.2

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.99
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 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 4326431 c.1042delC frameshift_variant 1.0 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 5659 p.Lys140Asn missense_variant 0.14
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9192 p.Leu631Val missense_variant 0.18
gyrA 9213 p.Thr638Ser missense_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9652 p.Ile784Thr missense_variant 0.29
fgd1 490828 p.Ala16Thr missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575432 p.Gly29Arg missense_variant 0.33
mshA 576606 p.Ala420Gly missense_variant 0.6
rpoB 759738 c.-69G>C upstream_gene_variant 0.29
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoB 761482 p.Ala559Gly missense_variant 0.5
rpoB 761651 p.Ser615Arg missense_variant 0.12
rpoB 762062 c.2256T>C synonymous_variant 0.18
rpoB 762319 p.Ser838Phe missense_variant 0.29
rpoB 762366 p.Glu854Lys missense_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 1.0
mmpL5 776612 c.1869C>T synonymous_variant 0.14
mmpS5 779603 c.-698C>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303155 c.225G>C synonymous_variant 0.25
fbiC 1305011 p.Val694Gly missense_variant 0.22
Rv1258c 1407127 p.Arg72Gly missense_variant 0.29
embR 1416430 c.918G>C synonymous_variant 0.38
embR 1416581 p.Arg256His missense_variant 0.11
embR 1416798 c.548_549delCG frameshift_variant 0.2
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.25
inhA 1674590 p.Met130Lys missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102817 p.Leu76Val missense_variant 0.29
katG 2154190 p.Leu641* stop_gained 0.2
katG 2154517 p.Ala532Val missense_variant 0.15
katG 2154667 p.Ser482Trp missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156172 c.-61G>A upstream_gene_variant 0.13
PPE35 2167916 c.2696delT frameshift_variant 0.25
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168111 c.2502C>T synonymous_variant 0.29
PPE35 2168816 c.1797C>G synonymous_variant 0.11
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.29
eis 2715480 c.-148C>T upstream_gene_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746525 c.1074G>C synonymous_variant 0.22
pepQ 2860112 p.Thr103Ala missense_variant 0.29
ribD 2987356 p.Val173Gly missense_variant 0.2
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3067147 c.-956A>C upstream_gene_variant 0.22
thyA 3074544 c.-73T>G upstream_gene_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087205 p.Leu129Gln missense_variant 0.25
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474052 p.Phe16Val missense_variant 0.4
fprA 3474390 p.Phe128Leu missense_variant 0.15
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474716 p.Asp237Ala missense_variant 0.22
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475303 p.Ala433Ser missense_variant 0.14
whiB7 3568433 p.Arg83Gly missense_variant 1.0
Rv3236c 3612870 p.Ala83Thr missense_variant 0.18
Rv3236c 3612942 p.Ala59Thr missense_variant 0.12
fbiA 3641288 p.Glu249Val missense_variant 0.29
ddn 3986728 c.-116T>C upstream_gene_variant 0.15
clpC1 4038951 p.Phe585Ser missense_variant 0.18
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240409 p.Pro183Ala missense_variant 0.8
embC 4240427 p.Ser189Cys missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241275 c.1413A>G synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247126 p.Thr205Pro missense_variant 0.33
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247659 c.1146C>T synonymous_variant 1.0
embB 4248328 c.1815G>C synonymous_variant 0.4
embB 4249009 c.2496G>A synonymous_variant 0.15
aftB 4267009 p.Leu610Met missense_variant 0.17
aftB 4267400 c.1437G>C synonymous_variant 0.15
aftB 4267705 p.Leu378Val missense_variant 0.67
aftB 4267972 p.Phe289Val missense_variant 0.18
aftB 4268619 p.Val73Gly missense_variant 0.3
aftB 4269321 c.-485G>A upstream_gene_variant 0.29
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326215 p.Glu420Ala missense_variant 0.33
ethA 4327440 p.Ala12Thr missense_variant 0.12
ethA 4328218 c.-745A>G upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0