TB-Profiler result

Run: SRR18910161

Summary

Run ID: SRR18910161

Sample name:

Date: 03-04-2023 20:38:38

Number of reads: 801753

Percentage reads mapped: 95.82

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 0.99
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8688 p.Ala463Thr missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576778 c.1431G>A synonymous_variant 0.14
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760404 p.Pro200Ala missense_variant 0.13
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765698 c.2332dupT frameshift_variant 0.12
rpoC 766891 c.3527delT frameshift_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775807 p.Met892Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777076 p.Ala469Ser missense_variant 0.12
mmpL5 779202 c.-722G>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473456 n.-202C>T upstream_gene_variant 0.11
rrl 1474252 n.595T>C non_coding_transcript_exon_variant 0.13
inhA 1674542 p.Ala114Val missense_variant 0.29
inhA 1674848 p.Gln216Arg missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101712 p.Gln444Leu missense_variant 0.11
ndh 2101792 p.Trp417Cys missense_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167792 p.Ser941Pro missense_variant 0.25
PPE35 2167865 c.2748G>C synonymous_variant 0.15
PPE35 2167868 c.2745A>C synonymous_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518406 p.Ala98Thr missense_variant 0.18
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746660 c.938delT frameshift_variant 0.25
Rv2752c 3065192 p.Ile334Val missense_variant 0.11
Rv2752c 3065388 c.804C>G synonymous_variant 0.12
Rv2752c 3066347 c.-156T>C upstream_gene_variant 0.14
Rv2752c 3067167 c.-976C>A upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087295 p.Leu159Pro missense_variant 0.11
Rv3083 3448331 c.-173G>C upstream_gene_variant 0.22
Rv3083 3448899 c.396C>A synonymous_variant 0.11
Rv3083 3449175 c.672C>T synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0