TB-Profiler result

Run: ERR2512525
Summary

Run ID: ERR2512525

Sample name:

Date: 31-03-2023 19:05:38

Number of reads: 910021

Percentage reads mapped: 98.8

Strain: lineage1.2.2.2

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
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.2 Indo-Oceanic NA 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 5075 c.-165C>T upstream_gene_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6897 p.Arg553Gln missense_variant 0.12
gyrA 7268 c.-34C>T upstream_gene_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 490901 c.123dupT frameshift_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575276 c.-72C>A upstream_gene_variant 0.11
mshA 576770 p.Arg475Ser missense_variant 0.11
ccsA 619907 p.Val6Ala missense_variant 0.14
ccsA 620079 c.189C>T synonymous_variant 0.22
rpoB 760512 p.Gly236Cys missense_variant 0.11
rpoB 762125 c.2319G>A synonymous_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 766885 c.3516G>T synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304472 c.1542T>C synonymous_variant 0.14
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473503 n.-155G>A upstream_gene_variant 0.13
rrl 1475702 n.2045G>T non_coding_transcript_exon_variant 0.67
inhA 1673628 c.-574C>T upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155300 p.Thr271Asn missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2170234 c.378delT frameshift_variant 1.0
PPE35 2170516 p.Gly33Arg missense_variant 0.88
Rv1979c 2222133 c.1032C>T synonymous_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289681 c.-440T>C upstream_gene_variant 0.12
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518440 p.Ala109Val missense_variant 0.18
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746265 p.Ser445* stop_gained 0.12
Rv2752c 3065020 p.Arg391His missense_variant 0.12
thyA 3074008 p.Ala155Asp missense_variant 0.11
thyA 3074633 c.-162C>T upstream_gene_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448822 p.Ala107Thr 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
Rv3236c 3612032 p.Met362Thr missense_variant 0.11
fbiB 3642765 p.Glu411Lys missense_variant 0.12
clpC1 4039311 p.Glu465Val missense_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4044198 c.84C>A synonymous_variant 0.12
panD 4044396 c.-115C>A upstream_gene_variant 0.14
embC 4240655 p.Ala265Pro missense_variant 0.24
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241028 p.Trp389* stop_gained 0.12
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241048 p.Leu396Phe missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243996 p.Ala255Glu missense_variant 0.1
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247360 p.Val283Met missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326148 c.1326G>T synonymous_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
whiB6 4338203 p.Arg107Cys 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
gid 4408429 c.-227A>T upstream_gene_variant 0.12