TB-Profiler result

Run: SRR19303885
Summary

Run ID: SRR19303885

Sample name:

Date: 03-04-2023 21:11:10

Number of reads: 3505263

Percentage reads mapped: 99.24

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 5530 c.291C>T synonymous_variant 1.0
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 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.32
ccsA 620586 c.696C>T synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764540 p.Val391Leu missense_variant 0.11
rpoC 765889 c.2520C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777155 c.1326G>C synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302948 c.18T>G synonymous_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472194 n.349G>A non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.41
PPE35 2170053 p.Thr187Ser missense_variant 0.43
PPE35 2170065 p.Ala183Gly missense_variant 0.19
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
kasA 2518518 p.Arg135Leu missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2747753 c.-155G>A upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.14
Rv2752c 3064889 p.Lys435Glu missense_variant 1.0
Rv2752c 3066103 p.Asn30Ser missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.5
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 3475159 p.Asn385Asp missense_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 1.0
alr 3841568 c.-148G>A upstream_gene_variant 1.0
alr 3841570 c.-151delA upstream_gene_variant 1.0
alr 3841574 c.-154T>G upstream_gene_variant 1.0
alr 3841578 c.-158G>T upstream_gene_variant 1.0
alr 3841582 c.-162A>G upstream_gene_variant 1.0
alr 3841584 c.-164C>A upstream_gene_variant 1.0
alr 3841589 c.-170delG upstream_gene_variant 1.0
alr 3841612 c.-193_-192insC upstream_gene_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.33
embB 4246548 p.Pro12Gln missense_variant 0.42
embB 4246555 c.42G>C synonymous_variant 0.42
embB 4246556 p.Ala15Pro missense_variant 0.42
embB 4246563 p.Leu17Trp missense_variant 0.22
embB 4246567 c.54G>T synonymous_variant 0.24
embB 4246584 p.Arg24Pro missense_variant 0.17
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248324 p.Ala604Gly missense_variant 0.2
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethA 4327704 c.-231C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
whiB6 4338635 c.-114A>C upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0