TB-Profiler result

Run: SRR7496481

Summary

Run ID: SRR7496481

Sample name:

Date: 04-04-2023 19:09:59

Number of reads: 388144

Percentage reads mapped: 99.44

Strain: lineage1.2.1.2.1

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
lineage1.2.1 Indo-Oceanic EAI2 RD239 1.0
lineage1.2.1.2 Indo-Oceanic NA RD239 1.0
lineage1.2.1.2.1 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 5605 c.366C>T synonymous_variant 0.17
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 8158 p.Ser286* stop_gained 0.29
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 1.0
rpoB 760010 c.204C>A synonymous_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764085 p.Asn239Ser missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777765 p.Gly239Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
embR 1417001 p.Val116Asp missense_variant 0.12
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473513 n.-145T>C upstream_gene_variant 0.33
rrl 1473676 n.19G>T non_coding_transcript_exon_variant 0.33
rrl 1474033 n.378_379delCG non_coding_transcript_exon_variant 0.29
rrl 1474521 n.864A>T non_coding_transcript_exon_variant 0.25
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 1.0
rrl 1474656 n.999G>A non_coding_transcript_exon_variant 0.22
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
inhA 1674362 p.Leu54Pro missense_variant 0.14
rpsA 1833404 c.-138G>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102658 p.Asp129Tyr missense_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167944 p.Ser890* stop_gained 0.17
PPE35 2168531 c.2082G>T synonymous_variant 0.22
PPE35 2169087 p.Pro509Leu missense_variant 0.17
PPE35 2169309 p.Gly435Asp missense_variant 1.0
PPE35 2169941 c.672C>A synonymous_variant 0.15
Rv1979c 2221778 p.Ala463Ser missense_variant 0.18
Rv1979c 2222204 p.Phe321Ile missense_variant 0.12
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222464 p.Gly234Val missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517923 c.-192C>A upstream_gene_variant 0.13
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519048 p.Gly312Ser missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064777 p.Phe472Ser missense_variant 0.14
Rv2752c 3064800 p.Glu464Asp missense_variant 0.15
thyA 3074218 c.253delA frameshift_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448985 c.484delC frameshift_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474136 p.Thr44Ala missense_variant 0.15
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568488 c.191delG frameshift_variant 1.0
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040811 c.-107C>A upstream_gene_variant 0.33
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 4243580 c.348G>A synonymous_variant 1.0
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247578 c.1065G>A synonymous_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
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
whiB6 4338361 p.Arg54Gln 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 4408149 c.54T>A synonymous_variant 0.14