TB-Profiler result

Run: ERR2513581
Summary

Run ID: ERR2513581

Sample name:

Date: 31-03-2023 19:46:29

Number of reads: 470378

Percentage reads mapped: 99.23

Strain: lineage1.1.1.1

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 0.99
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.99
lineage1.1.1.1 Indo-Oceanic EAI4;ZERO 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 6112 p.Met291Ile missense_variant 1.0
gyrB 6343 p.Glu368Asp missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8227 p.Arg309Gln missense_variant 0.14
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 490751 c.-32T>G upstream_gene_variant 0.43
fgd1 490972 p.Arg64Ser missense_variant 1.0
fgd1 491027 p.Asn82Thr missense_variant 0.36
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575806 c.459G>T synonymous_variant 0.12
mshA 576416 p.Leu357Met missense_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.88
rpoC 763886 c.517C>A synonymous_variant 0.88
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776089 p.Val798Ile missense_variant 0.18
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776766 p.Ala572Val missense_variant 0.17
mmpL5 777351 p.Arg377Leu missense_variant 0.29
mmpL5 777581 p.Tyr300* stop_gained 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801287 p.Val160Gly missense_variant 0.22
fbiC 1303016 p.Val29Gly missense_variant 0.36
fbiC 1303303 p.Pro125Thr missense_variant 0.13
embR 1416401 p.Asn316Ser missense_variant 0.15
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 1.0
fabG1 1673474 p.Pro12Leu missense_variant 0.22
rpsA 1833360 c.-182G>A upstream_gene_variant 0.29
rpsA 1834319 p.Val260Ile missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918289 p.Gln117Arg missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156389 c.-278G>C upstream_gene_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168270 c.2343G>C synonymous_variant 0.13
PPE35 2169293 c.1320T>G synonymous_variant 0.22
PPE35 2170048 p.Leu189Val missense_variant 0.29
PPE35 2170053 p.Thr187Ser missense_variant 0.29
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222439 c.726C>T synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290221 c.-980C>A upstream_gene_variant 0.22
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.33
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyA 3074030 p.Ala148Thr missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087035 c.216C>A synonymous_variant 0.12
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449527 p.Ile342Phe missense_variant 0.14
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 3568540 p.Pro47Leu missense_variant 0.17
whiB7 3568742 c.-63C>A upstream_gene_variant 0.15
fbiB 3642029 c.495C>A synonymous_variant 0.17
rpoA 3877599 p.Gln303His missense_variant 0.15
clpC1 4038420 p.Arg762Leu missense_variant 0.15
clpC1 4040350 p.Val119Leu missense_variant 0.15
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240766 c.904C>A synonymous_variant 0.17
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.29
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244096 c.864C>T synonymous_variant 0.92
embA 4244720 c.1488C>T synonymous_variant 1.0
embA 4244879 c.1647C>G synonymous_variant 1.0
embA 4245761 p.Tyr843* stop_gained 0.22
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 0.94
embB 4248112 c.1599C>T synonymous_variant 0.14
embB 4248848 p.Pro779Ser missense_variant 0.12
aftB 4268013 p.Pro275Gln missense_variant 0.17
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
aftB 4269609 c.-773G>A upstream_gene_variant 0.14
ubiA 4269663 p.Met57Ile missense_variant 0.13
ethA 4326212 p.Arg421Gln missense_variant 0.11
ethA 4326452 p.Ala341Glu missense_variant 0.12
whiB6 4338242 p.Gln94Glu missense_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 4407873 c.330G>T synonymous_variant 1.0