TB-Profiler result

Run: SRR7496484
Summary

Run ID: SRR7496484

Sample name:

Date: 04-04-2023 19:10:45

Number of reads: 304349

Percentage reads mapped: 99.2

Strain: lineage1.2.1.2.1

Drug-resistance: Other

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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
lineage1.2.1 Indo-Oceanic EAI2 RD239 1.0
lineage1.2.1.2 Indo-Oceanic NA RD239 1.0
lineage1.2.1.2.1 Indo-Oceanic NA RD239 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
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
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 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490720 c.-63T>G upstream_gene_variant 1.0
fgd1 491368 p.Ser196Thr missense_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 1.0
ccsA 620221 p.Tyr111Asn missense_variant 0.13
rpoB 760288 p.Ile161Thr missense_variant 0.11
rpoB 760337 c.535dupG frameshift_variant 0.13
rpoB 760595 c.789C>T synonymous_variant 0.13
rpoB 760664 c.858G>A synonymous_variant 0.12
rpoB 762667 p.Pro954Arg missense_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765450 p.Ala694Asp missense_variant 0.11
rpoC 767223 p.Ile1285Asn missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777718 p.Ile255Val missense_variant 0.11
mmpL5 777882 p.Gly200Val missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303014 c.84G>A synonymous_variant 0.13
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.6
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417418 c.-119_-72delTACATCGCACGGCGTGCCGAGATCCTGGGTTCTTACCGCATCGGCGAA upstream_gene_variant 1.0
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 1.0
rrl 1475920 n.2263G>A non_coding_transcript_exon_variant 0.11
rrl 1476200 n.2543A>G non_coding_transcript_exon_variant 0.11
rrl 1476643 n.2986A>G non_coding_transcript_exon_variant 0.13
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
tlyA 1917914 c.-26G>A upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155314 c.798C>T synonymous_variant 0.18
katG 2155472 c.640C>A synonymous_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168198 c.2415G>A synonymous_variant 1.0
PPE35 2169757 p.Asn286Asp missense_variant 0.12
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519048 p.Gly312Ser missense_variant 1.0
eis 2715369 c.-37G>A upstream_gene_variant 0.14
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726416 p.Phe75Tyr missense_variant 0.14
folC 2746860 p.Ala247Ser missense_variant 0.11
folC 2747722 c.-125delG upstream_gene_variant 0.11
folC 2747754 c.-156C>T upstream_gene_variant 0.12
thyA 3074366 p.Tyr36His missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087690 p.His291Tyr missense_variant 0.11
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448657 p.Gly52Arg missense_variant 0.12
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473901 c.-106G>T upstream_gene_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568488 c.191delG frameshift_variant 1.0
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
alr 3840561 p.Ile287Thr missense_variant 0.11
rpoA 3878039 p.Ala157Ser missense_variant 0.12
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 4241109 p.Ala416Glu missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248253 c.1740C>A synonymous_variant 0.11
embB 4248961 c.2448T>C synonymous_variant 0.11
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269764 p.Arg24Cys missense_variant 0.13
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
whiB6 4338361 p.Arg54Gln 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
fbiC 1305494 c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN frameshift_variant&stop_lost&splice_region_variant 1.0