TB-Profiler result

Run: SRR11972207
Summary

Run ID: SRR11972207

Sample name:

Date: 03-04-2023 05:31:58

Number of reads: 293158

Percentage reads mapped: 99.13

Strain: lineage1.1.1

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
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.97
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 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490980 c.198C>T synonymous_variant 0.25
fgd1 491066 c.286delC frameshift_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 761770 p.Met655Thr missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781477 c.-83G>A upstream_gene_variant 0.15
fbiC 1304998 p.Trp690Arg missense_variant 0.14
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1461018 c.-27A>G upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 1.0
rrl 1475450 n.1793C>T non_coding_transcript_exon_variant 0.17
rrl 1476615 n.2958T>A non_coding_transcript_exon_variant 0.18
rpsA 1834315 c.774C>T synonymous_variant 1.0
rpsA 1834319 p.Val260Ile missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102342 p.Ala234Asp missense_variant 0.15
ndh 2102487 p.Ala186Ser missense_variant 0.12
ndh 2103022 c.21C>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155448 p.Ala222Thr missense_variant 0.22
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223144 p.Arg7Ser missense_variant 0.94
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518123 c.9G>A synonymous_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2714403 c.930C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
pepQ 2860405 p.Gln5Arg missense_variant 0.12
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyA 3074308 p.Val55Ala missense_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339479 p.Gln121Arg missense_variant 0.15
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449884 p.Arg461Trp missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.9
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612902 p.Ala72Val missense_variant 0.2
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038890 c.1815G>A synonymous_variant 0.12
clpC1 4039064 c.1640delG frameshift_variant 0.14
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241783 p.Trp641Arg missense_variant 0.25
embC 4242007 c.2145G>A synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.2
embA 4243720 p.Pro163Leu missense_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244096 c.864C>T synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246491 p.Pro1087Ser missense_variant 1.0
embB 4247534 p.Thr341Ser missense_variant 0.15
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4268346 p.Ala164Val missense_variant 0.15
aftB 4268362 p.Ser159Thr missense_variant 0.17
aftB 4268379 p.Trp153* stop_gained 0.17
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326312 p.Asn388Asp missense_variant 0.18
ethA 4327774 c.-301G>A upstream_gene_variant 0.11
whiB6 4338242 p.Gln94Glu 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