TB-Profiler result

Run: SRR8791320
Summary

Run ID: SRR8791320

Sample name:

Date: 04-04-2023 21:56:25

Number of reads: 235022

Percentage reads mapped: 98.83

Strain:

Drug-resistance: HR-TB

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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
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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289054 p.Asp63Ala missense_variant 1.0 pyrazinamide
ddn 3987106 p.Trp88* stop_gained 1.0 delamanid
embB 4247574 p.Asp354Ala missense_variant 1.0 ethambutol
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 5206 c.-34C>A upstream_gene_variant 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8266 p.Ala322Val missense_variant 0.33
gyrA 8380 p.Gln360Arg missense_variant 0.29
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9431 c.2130G>T synonymous_variant 0.33
gyrA 9476 c.2175G>T synonymous_variant 0.33
gyrA 9484 p.Ser728* stop_gained 0.33
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575339 c.-9C>T upstream_gene_variant 0.33
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620447 p.Phe186Ser missense_variant 0.17
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620725 p.Leu279Met missense_variant 0.2
rpoB 760177 p.Ala124Glu missense_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765179 p.Gly604Trp missense_variant 0.25
rpoC 765546 p.Arg726His missense_variant 1.0
rpoC 765680 p.Asn771Asp missense_variant 0.5
rpoC 765698 p.Ile777Val missense_variant 0.5
rpoC 766802 p.Gln1145* stop_gained 0.25
rpoC 767102 p.Leu1245Ile missense_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777484 p.Gln333Lys missense_variant 0.25
mmpL5 778231 p.Glu84* stop_gained 0.29
mmpR5 778238 c.-752C>A upstream_gene_variant 0.22
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302889 c.-42G>T upstream_gene_variant 1.0
fbiC 1303547 p.Pro206Gln missense_variant 0.5
fbiC 1304164 p.Gly412* stop_gained 0.2
fbiC 1304585 p.Ile552Asn missense_variant 0.25
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406894 c.447C>T synonymous_variant 0.4
rrs 1471656 n.-190G>T upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472115 n.270C>G non_coding_transcript_exon_variant 0.25
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.33
rrs 1472313 n.468G>T non_coding_transcript_exon_variant 0.67
rrl 1474164 n.507C>A non_coding_transcript_exon_variant 0.2
rrl 1474590 n.933A>G non_coding_transcript_exon_variant 0.5
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.18
rrl 1474933 n.1276A>C non_coding_transcript_exon_variant 0.33
rrl 1475637 n.1980T>C non_coding_transcript_exon_variant 0.22
fabG1 1673165 c.-275A>G upstream_gene_variant 1.0
inhA 1674629 p.Ser143Tyr missense_variant 0.25
inhA 1674673 p.Tyr158His missense_variant 0.25
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834934 p.Ala465Ser missense_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102071 c.972C>A synonymous_variant 0.25
ndh 2102114 p.Ser310Tyr missense_variant 0.25
ndh 2102591 p.Ile151Thr missense_variant 0.25
ndh 2102850 p.Glu65Lys missense_variant 1.0
katG 2154045 p.Trp689Cys missense_variant 0.29
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155529 p.Glu195* stop_gained 0.5
katG 2155834 p.Ala93Gly missense_variant 0.67
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168288 c.2325C>A synonymous_variant 0.29
PPE35 2168326 p.Asp763Asn missense_variant 0.29
PPE35 2168435 c.2178C>A synonymous_variant 0.33
PPE35 2168494 p.Gly707Cys missense_variant 0.4
PPE35 2169057 p.Pro519Arg missense_variant 0.4
PPE35 2169926 c.687C>T synonymous_variant 0.29
Rv1979c 2221809 c.1356C>A synonymous_variant 0.15
Rv1979c 2222520 p.Lys215Asn missense_variant 0.33
Rv1979c 2222845 p.Gly107Val missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288937 p.Ala102Val missense_variant 0.33
pncA 2289906 c.-665T>C upstream_gene_variant 0.33
kasA 2518887 p.Gly258Asp missense_variant 0.25
eis 2714155 p.Asp393Gly missense_variant 0.33
ribD 2987035 p.Gly66Asp missense_variant 0.22
ribD 2987230 p.Ala131Val missense_variant 0.2
Rv2752c 3065966 p.Ala76Ser missense_variant 0.5
Rv2752c 3066275 c.-84G>A upstream_gene_variant 0.33
thyX 3067634 c.312C>A synonymous_variant 0.33
thyX 3067662 p.Arg95Leu missense_variant 0.25
thyA 3073928 p.Ala182Ser missense_variant 0.25
thyA 3074264 p.Gly70Ser missense_variant 0.2
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087018 p.Asp67Asn missense_variant 0.33
fbiD 3339614 p.Ser166* stop_gained 0.5
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474342 c.336G>A synonymous_variant 0.4
fprA 3474412 p.Pro136Thr missense_variant 0.17
Rv3236c 3613149 c.-33G>T upstream_gene_variant 0.25
alr 3841078 p.Pro115Thr missense_variant 0.17
alr 3841115 c.306T>G synonymous_variant 0.17
rpoA 3877956 p.Glu184Asp missense_variant 1.0
ddn 3987084 p.Gly81Cys missense_variant 0.33
clpC1 4038646 p.Glu687* stop_gained 0.14
clpC1 4039591 p.Val372Leu missense_variant 0.18
clpC1 4040479 p.Gly76Arg missense_variant 0.4
clpC1 4040724 c.-20G>T upstream_gene_variant 0.25
embC 4240478 p.Gly206Trp missense_variant 0.25
embC 4240542 p.Thr227Lys missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244401 p.Leu390Pro missense_variant 1.0
embB 4245956 c.-558G>T upstream_gene_variant 0.5
embA 4246425 p.Pro1065Ser missense_variant 0.5
embB 4248903 p.Thr797Lys missense_variant 0.25
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268623 p.Trp72Arg missense_variant 0.5
ubiA 4269707 p.Gly43Ser missense_variant 0.2
ubiA 4269756 p.Trp26Cys missense_variant 0.2
ubiA 4269882 c.-49G>T upstream_gene_variant 0.18
whiB6 4338185 p.Ala113Pro missense_variant 0.5
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0