TB-Profiler result

Run: SRR4034653
Summary

Run ID: SRR4034653

Sample name:

Date: 04-04-2023 06:56:57

Number of reads: 686688

Percentage reads mapped: 99.47

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7992 p.Ala231Thr missense_variant 0.17
gyrA 8903 c.1603delC frameshift_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9773 c.2472C>T synonymous_variant 0.29
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575549 p.Met68Val missense_variant 0.14
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759621 c.-186C>T upstream_gene_variant 0.15
rpoB 759994 p.Arg63His missense_variant 0.13
rpoB 760657 p.Glu284Val missense_variant 0.22
rpoB 761815 p.Ala670Val missense_variant 0.17
rpoB 762597 p.Gly931Arg missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765997 c.2628T>G synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 778147 p.Met112Val missense_variant 0.15
mmpL5 778161 p.Ala107Val missense_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781833 c.278_279delTG frameshift_variant 0.22
fbiC 1302776 c.-155C>T upstream_gene_variant 0.14
fbiC 1302891 c.-40G>A upstream_gene_variant 0.17
fbiC 1302992 c.65delA frameshift_variant 0.12
fbiC 1303843 p.Ala305Thr missense_variant 0.12
fbiC 1303953 c.1023C>T synonymous_variant 0.25
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
atpE 1461151 p.Ile36Asn missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472776 n.931A>G non_coding_transcript_exon_variant 0.14
rrl 1475612 n.1955G>T non_coding_transcript_exon_variant 0.13
rrl 1476076 n.2419A>G non_coding_transcript_exon_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918581 c.642G>C synonymous_variant 0.14
ndh 2102029 p.Gln338His missense_variant 0.17
ndh 2102139 p.Arg302Trp missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155431 c.681G>T synonymous_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169476 c.1137C>T synonymous_variant 0.12
PPE35 2169682 c.930delC frameshift_variant 0.11
PPE35 2170158 p.Ala152Val missense_variant 0.2
Rv1979c 2222778 c.387C>T synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290222 c.-981C>G upstream_gene_variant 0.2
folC 2747123 p.Ala159Val missense_variant 0.12
pepQ 2860094 p.Ala109Thr missense_variant 0.4
Rv2752c 3064711 c.1480delT frameshift_variant 0.12
Rv2752c 3067080 c.-890delT upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612331 c.786G>A synonymous_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641332 p.Gly264Arg missense_variant 1.0
fbiB 3642547 p.Gly338Val missense_variant 0.11
clpC1 4040174 c.530delA frameshift_variant 0.14
clpC1 4040616 p.Thr30Ile missense_variant 0.2
embC 4241335 c.1473G>A synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267483 c.1354T>C synonymous_variant 0.25
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethR 4328134 p.Glu196Lys missense_variant 0.29
whiB6 4338186 c.336T>C synonymous_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0