TB-Profiler result

Run: ERR4815964

Summary

Run ID: ERR4815964

Sample name:

Date: 01-04-2023 14:09:53

Number of reads: 731261

Percentage reads mapped: 99.41

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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
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
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 491742 c.960T>C synonymous_variant 1.0
mshA 575548 c.201C>T synonymous_variant 0.14
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765070 c.1701G>T synonymous_variant 0.12
rpoC 765331 p.Ser654Arg missense_variant 0.11
rpoC 766582 c.3213C>A synonymous_variant 1.0
rpoC 766929 p.Glu1187Gly missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775910 c.2571G>T synonymous_variant 0.13
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777557 c.924T>C synonymous_variant 0.11
mmpR5 779020 p.Gly11Cys missense_variant 0.2
mmpR5 779119 p.Leu44Met missense_variant 0.11
mmpR5 779447 p.Ala153Val missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303648 c.719delT frameshift_variant 0.17
Rv1258c 1407271 p.Gly24Cys missense_variant 1.0
embR 1416801 p.Ala183Thr missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475386 n.1729G>T non_coding_transcript_exon_variant 0.11
rrl 1476022 n.2365A>G non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155158 p.Glu318Asp missense_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2289758 c.-517G>A upstream_gene_variant 0.13
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746241 p.Asp453Val missense_variant 0.14
thyX 3067687 p.Arg87* stop_gained 0.13
thyX 3067883 c.63C>T synonymous_variant 0.12
thyX 3067918 p.Gln10* stop_gained 0.11
thyA 3074598 c.-127A>T upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087369 p.Ala184Ser missense_variant 0.14
ald 3087438 p.Leu207Phe missense_variant 0.25
fbiD 3339426 c.309T>C synonymous_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474111 c.105C>T synonymous_variant 0.17
fprA 3474315 c.309C>T synonymous_variant 0.15
Rv3236c 3612884 c.232delT frameshift_variant 0.18
fbiA 3640606 p.Leu22Met missense_variant 0.11
fbiB 3640746 c.-789C>T upstream_gene_variant 1.0
fbiB 3641670 p.Val46Leu missense_variant 0.17
fbiB 3641680 p.Thr49Ile missense_variant 0.17
alr 3840315 p.Gly369Asp missense_variant 0.11
alr 3840752 c.669C>T synonymous_variant 0.14
alr 3841473 c.-53G>A upstream_gene_variant 1.0
rpoA 3878438 p.Glu24* stop_gained 0.15
rpoA 3878492 p.Arg6Ser missense_variant 0.29
rpoA 3878552 c.-45C>A upstream_gene_variant 0.4
clpC1 4038174 c.2530dupG frameshift_variant 0.17
clpC1 4039559 c.1146C>T synonymous_variant 0.17
embC 4241138 p.Ala426Ser missense_variant 0.13
embC 4241530 c.1668C>A synonymous_variant 0.18
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242581 p.Ala907Ser missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244351 c.1119G>A synonymous_variant 0.13
aftB 4268252 c.585G>T synonymous_variant 0.17
ethA 4326040 c.1434G>A synonymous_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0