TB-Profiler result

Run: ERR2514427
Summary

Run ID: ERR2514427

Sample name:

Date: 31-03-2023 20:19:42

Number of reads: 339224

Percentage reads mapped: 99.24

Strain: lineage1.1.3

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
lineage1 Indo-Oceanic EAI RD239 0.97
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.98
lineage1.1.3 Indo-Oceanic EAI6 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
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 5436 p.Asn66Ser missense_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6114 p.Gln292Leu missense_variant 0.2
gyrB 7252 c.2015delT frameshift_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8423 c.1122G>A synonymous_variant 0.14
gyrA 8452 p.Ala384Val missense_variant 0.93
gyrA 8721 p.Arg474Trp missense_variant 0.13
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760260 p.Pro152Ser missense_variant 0.11
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
rpoC 765230 p.Ala621Thr missense_variant 1.0
rpoC 765564 p.Ser732Leu missense_variant 0.15
rpoC 766102 c.2733C>T synonymous_variant 0.18
rpoC 766541 p.Gly1058Ser missense_variant 0.12
rpoC 766676 p.Asp1103His missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776531 c.1950G>A synonymous_variant 0.13
mmpL5 776643 p.Met613Thr missense_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407194 p.Ser49Arg missense_variant 1.0
embR 1416198 c.1149delG frameshift_variant 0.12
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673916 c.-286A>G upstream_gene_variant 0.13
rpsA 1834831 c.1290G>A synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102287 c.756C>G synonymous_variant 0.18
ndh 2102397 p.Ala216Thr missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155471 p.Arg214Gln missense_variant 0.22
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2170753 c.-141T>C upstream_gene_variant 0.11
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517924 c.-191G>A upstream_gene_variant 0.12
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2714569 p.Ala255Gly missense_variant 0.29
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726226 p.Ala12Thr missense_variant 0.15
folC 2747577 p.Pro8Ser missense_variant 0.17
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065540 p.Val218Leu missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568513 p.Ala56Val missense_variant 0.25
fbiA 3641020 p.Val160Ile missense_variant 0.2
fbiB 3642131 c.597C>T synonymous_variant 0.25
alr 3840297 p.Thr375Met missense_variant 0.11
alr 3840299 c.1122C>T synonymous_variant 1.0
alr 3841244 c.177G>A synonymous_variant 0.11
ddn 3986744 c.-100C>T upstream_gene_variant 0.29
clpC1 4038543 p.Gln721Pro missense_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240648 c.786C>T synonymous_variant 0.29
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241815 c.1953G>T synonymous_variant 0.25
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 4247646 p.Glu378Ala missense_variant 1.0
embB 4248360 p.Pro616Gln missense_variant 0.18
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269868 c.-35G>T upstream_gene_variant 0.13
whiB6 4338243 c.278delG frameshift_variant 1.0
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 4407780 c.423G>A synonymous_variant 0.93
gid 4407873 c.330G>T synonymous_variant 0.88