TB-Profiler result

Run: SRR6982457
Summary

Run ID: SRR6982457

Sample name:

Date: 04-04-2023 18:38:04

Number of reads: 737635

Percentage reads mapped: 99.37

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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576489 p.Val381Ala missense_variant 0.1
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.25
ccsA 620752 p.Arg288Gly missense_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764042 p.Thr225Ala missense_variant 0.13
rpoC 766500 p.Ala1044Val missense_variant 0.96
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 778885 c.-405T>C upstream_gene_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
atpE 1460876 c.-169G>T upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475178 n.1521T>C non_coding_transcript_exon_variant 0.12
rrl 1475857 n.2200C>A non_coding_transcript_exon_variant 0.14
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.12
fabG1 1673357 c.-83G>A upstream_gene_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.12
rpsA 1833749 p.Ile70Leu missense_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102134 c.909C>A synonymous_variant 0.17
ndh 2103160 c.-118C>A upstream_gene_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155228 p.Gln295Ala missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168213 c.2400G>T synonymous_variant 0.17
PPE35 2168234 c.2379G>T synonymous_variant 0.17
PPE35 2168521 p.Gln698Lys missense_variant 0.18
PPE35 2169796 p.Gly273Cys missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.18
PPE35 2170053 p.Thr187Ser missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714526 c.805_806delAC frameshift_variant 1.0
Rv2752c 3065711 p.Gly161Ser missense_variant 1.0
thyA 3074414 p.Asp20Tyr missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339333 c.216G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
ddn 3986778 c.-66G>T upstream_gene_variant 0.15
embC 4242317 p.Glu819* stop_gained 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4249570 c.3057G>T synonymous_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267931 c.906C>A 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