TB-Profiler result

Run: SRR6046556
Summary

Run ID: SRR6046556

Sample name:

Date: 04-04-2023 12:18:49

Number of reads: 1001515

Percentage reads mapped: 99.17

Strain: lineage1.2.2.2

Drug-resistance: HR-TB

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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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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
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 7839 p.Gly180Ser missense_variant 0.12
gyrA 7935 p.Glu212Lys missense_variant 1.0
gyrA 7943 p.Glu214Asp 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 491742 c.960T>C synonymous_variant 1.0
mshA 576067 c.720C>T synonymous_variant 0.14
mshA 576195 p.Val283Glu missense_variant 0.2
mshA 576751 p.Lys468Asn missense_variant 0.22
rpoB 762171 p.Glu789Lys missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763528 c.159G>A synonymous_variant 0.11
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764656 c.1287C>A synonymous_variant 0.13
rpoC 766245 p.Gln959Pro missense_variant 0.11
rpoC 766941 p.Arg1191His missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779243 p.Val85Ala missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303115 p.Ala62Val missense_variant 0.11
fbiC 1303152 c.222C>A synonymous_variant 0.11
fbiC 1304246 p.Asp439Val missense_variant 0.13
Rv1258c 1407402 c.-62C>T upstream_gene_variant 0.12
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1461143 c.99C>T synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476766 n.3109C>A non_coding_transcript_exon_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102144 p.Ala300Asp missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155309 p.Gly268Val missense_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2168855 c.1758T>A synonymous_variant 0.12
PPE35 2170392 p.Gly74Ala missense_variant 0.13
PPE35 2170400 c.213G>C synonymous_variant 0.14
Rv1979c 2222014 p.Val384Ala missense_variant 0.11
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222395 p.Pro257Gln missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289875 c.-634C>A upstream_gene_variant 0.13
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518391 p.Gln93* stop_gained 0.14
eis 2714855 p.Gly160Ser missense_variant 0.22
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2747547 p.Val18Met missense_variant 0.13
pepQ 2859347 p.Thr358Ala missense_variant 0.11
pepQ 2859579 c.840G>A synonymous_variant 0.17
Rv2752c 3064785 c.1407G>A synonymous_variant 0.15
thyX 3067790 c.156C>G synonymous_variant 0.11
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 3474767 p.Gly254Val missense_variant 0.13
fprA 3475159 p.Asn385Asp missense_variant 1.0
rpoA 3878641 c.-135delG upstream_gene_variant 0.18
ddn 3986819 c.-25A>C upstream_gene_variant 0.12
clpC1 4039423 p.Ile428Val missense_variant 0.13
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240993 c.1131G>T synonymous_variant 0.13
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241536 c.1674A>G synonymous_variant 0.11
embC 4241617 p.Lys585Asn missense_variant 0.11
embC 4242571 p.Asp903Glu missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242711 p.Gln950Arg missense_variant 0.1
embA 4243946 c.714C>T synonymous_variant 0.15
embA 4243981 p.Ser250Asn missense_variant 0.12
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4268038 p.Trp267Arg missense_variant 0.11
aftB 4268612 c.225G>T synonymous_variant 0.5
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.21
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 4407808 p.Asp132Val missense_variant 0.12
gid 4407873 c.330G>T synonymous_variant 1.0