TB-Profiler result

Run: ERR2513527
Summary

Run ID: ERR2513527

Sample name:

Date: 31-03-2023 19:44:20

Number of reads: 6816291

Percentage reads mapped: 99.39

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 1.0
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 5119 c.-121T>G upstream_gene_variant 0.41
gyrB 6112 p.Met291Ile missense_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 9304 p.Gly668Asp missense_variant 1.0
fgd1 490813 p.Ser11Pro missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575769 p.Ala141Val missense_variant 0.13
mshA 575821 c.474G>A synonymous_variant 0.15
mshA 575858 p.Val171Met missense_variant 0.2
mshA 576653 p.Ala436Thr missense_variant 0.22
ccsA 619827 c.-64C>T upstream_gene_variant 0.18
ccsA 620130 c.240G>T synonymous_variant 0.33
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 0.99
rpoC 765230 p.Ala621Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 0.99
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776974 p.Met503Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304088 p.Tyr386* stop_gained 0.12
fbiC 1304242 p.Pro438Thr missense_variant 0.33
fbiC 1304265 c.1335C>T synonymous_variant 0.29
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918205 p.Ala89Glu missense_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
Rv1979c 2221801 p.Thr455Lys missense_variant 1.0
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
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ribD 2987386 p.Ala183Val missense_variant 0.19
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyX 3067454 c.492C>T synonymous_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339560 p.Thr148Asn missense_variant 0.14
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449727 c.1224G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474945 c.939G>A synonymous_variant 0.23
fprA 3475159 p.Asn385Asp missense_variant 0.99
fprA 3475322 p.Arg439Leu missense_variant 0.22
alr 3840993 p.His143Arg missense_variant 0.18
alr 3841154 c.267C>A synonymous_variant 1.0
alr 3841253 c.168C>T synonymous_variant 0.99
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240582 c.720C>T synonymous_variant 0.33
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242543 p.Arg894Leu missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244400 p.Leu390Met missense_variant 0.17
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247026 c.513G>A synonymous_variant 0.18
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248587 p.Gly692Ser missense_variant 0.13
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 0.99
gid 4407588 c.615A>G synonymous_variant 0.99
gid 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 1.0