TB-Profiler result

Run: SRR12199395
Summary

Run ID: SRR12199395

Sample name:

Date: 03-04-2023 06:37:10

Number of reads: 298513

Percentage reads mapped: 94.57

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 0.99
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 6960 p.Gln574Arg missense_variant 0.9
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
gyrA 9406 p.Gly702Asp missense_variant 0.22
fgd1 491742 c.960T>C synonymous_variant 1.0
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
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777256 p.Pro409Thr missense_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416311 p.Ser346Leu missense_variant 0.25
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.5
rrs 1472619 n.774C>T non_coding_transcript_exon_variant 0.33
rrs 1472620 n.775A>G non_coding_transcript_exon_variant 0.33
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.25
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.3
inhA 1674619 p.Pro140Ala missense_variant 1.0
rpsA 1833353 c.-189C>A upstream_gene_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918555 p.Arg206Trp missense_variant 0.25
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 2169220 c.1393C>T synonymous_variant 0.33
PPE35 2169237 p.Asp459Gly missense_variant 0.4
PPE35 2169488 c.1125G>C synonymous_variant 0.25
PPE35 2169491 c.1122T>C synonymous_variant 0.25
PPE35 2169902 p.Leu237Phe missense_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.67
PPE35 2170053 p.Thr187Ser missense_variant 0.59
PPE35 2170528 p.Ser29Ala missense_variant 0.25
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ribD 2986713 c.-126A>C upstream_gene_variant 0.29
ribD 2987150 p.Gln104His missense_variant 0.4
Rv2752c 3065354 p.Arg280* stop_gained 0.17
thyA 3074648 c.-177T>G upstream_gene_variant 0.33
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 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612883 c.234T>C synonymous_variant 0.33
fbiA 3640375 c.-168C>A upstream_gene_variant 0.22
rpoA 3877595 p.Gly305Ser missense_variant 0.29
rpoA 3877698 p.His270Gln missense_variant 0.2
rpoA 3877722 c.786C>T synonymous_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 4247512 c.999T>C synonymous_variant 0.2
embB 4247516 p.Asn335Asp missense_variant 0.2
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248160 c.1647C>T synonymous_variant 0.25
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