TB-Profiler result

Run: SRR11972213
Summary

Run ID: SRR11972213

Sample name:

Date: 03-04-2023 05:32:12

Number of reads: 538709

Percentage reads mapped: 98.52

Strain: lineage1.1.3.1

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 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.99
lineage1.1.3.1 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 5117 c.-123G>A upstream_gene_variant 0.5
gyrB 5415 p.Ala59Val missense_variant 0.12
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 6478 c.-824G>A upstream_gene_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7415 c.114C>A synonymous_variant 0.17
gyrA 7434 p.Arg45Cys missense_variant 0.18
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7852 p.Gly184Asp missense_variant 0.13
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 491104 p.Gly108Arg missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 761385 p.Ala527Ser missense_variant 0.14
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 763922 p.Glu185* stop_gained 0.17
rpoC 764451 p.Gly361Asp missense_variant 0.11
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777572 c.909C>T synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305427 c.2497C>T synonymous_variant 0.12
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.12
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 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2170385 c.228G>T synonymous_variant 0.2
PPE35 2170392 p.Gly74Ala missense_variant 0.18
PPE35 2170400 c.213G>C synonymous_variant 0.18
PPE35 2170435 p.Arg60Trp missense_variant 0.15
PPE35 2170509 p.Ala35Val missense_variant 0.13
PPE35 2170628 c.-16C>T upstream_gene_variant 0.12
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289403 c.-162T>A upstream_gene_variant 0.14
pncA 2289443 c.-202C>T upstream_gene_variant 0.17
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518512 p.Gly133Ala missense_variant 0.11
kasA 2518948 c.834G>A synonymous_variant 0.18
eis 2715357 c.-25G>A upstream_gene_variant 0.12
eis 2715453 c.-121C>T upstream_gene_variant 0.16
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3064722 c.1469delC frameshift_variant 0.12
Rv2752c 3067032 c.-841C>T upstream_gene_variant 0.36
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448402 c.-102C>A upstream_gene_variant 0.17
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
Rv3236c 3612592 p.Asp175Glu missense_variant 0.13
alr 3840375 p.Asp349Val missense_variant 0.11
alr 3841253 c.168C>T synonymous_variant 1.0
alr 3841277 c.144C>T synonymous_variant 1.0
rpoA 3878586 c.-79A>G upstream_gene_variant 0.56
rpoA 3878613 c.-113_-107delCAACCCA upstream_gene_variant 0.5
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240164 p.Gly101Asp missense_variant 0.2
embC 4240235 p.Arg125Trp missense_variant 0.22
embC 4240671 p.Thr270Ile missense_variant 0.9
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242784 c.-449G>C upstream_gene_variant 0.12
embA 4243478 c.246G>A synonymous_variant 0.15
embA 4243557 p.Ala109Thr missense_variant 0.18
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244217 p.Thr329Ser missense_variant 0.12
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246098 p.Phe956Ile missense_variant 0.13
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248341 p.Thr610Ala missense_variant 0.11
embB 4248504 p.Asp664Val missense_variant 0.15
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326914 p.Ala187Val missense_variant 0.15
ethR 4327456 c.-93G>A upstream_gene_variant 0.12
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408239 c.-37A>T upstream_gene_variant 0.12
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 1.0