TB-Profiler result

Run: SRR11972251
Summary

Run ID: SRR11972251

Sample name:

Date: 03-04-2023 05:33:30

Number of reads: 263189

Percentage reads mapped: 99.26

Strain: lineage1.1.2

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1.2 Indo-Oceanic EAI3;EAI5 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
katG 2154188 c.1923delA frameshift_variant 0.2 isoniazid
gid 4407851 c.351delG frameshift_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 5425 c.186A>T synonymous_variant 0.29
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 6775 c.-527G>A upstream_gene_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7495 p.Arg65His missense_variant 0.15
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 9289 p.Val663Glu missense_variant 0.29
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575990 p.Val215Ile missense_variant 0.22
rpoB 759956 c.150C>A synonymous_variant 0.17
rpoB 760446 p.Asp214Asn missense_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763077 p.Val1091Phe missense_variant 0.17
rpoB 763321 p.Ala1172Val missense_variant 0.13
rpoC 763479 p.Arg37Leu missense_variant 0.18
rpoC 763579 c.212delA frameshift_variant 0.2
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 763948 c.579G>T synonymous_variant 0.22
rpoC 764394 p.Asp342Val missense_variant 0.4
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765505 c.2136C>A synonymous_variant 0.29
rpoC 766732 c.3363G>A synonymous_variant 0.15
rpoC 766951 c.3582G>A synonymous_variant 0.5
rpoC 767160 p.Ile1264Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776973 c.1482_1507delCACCTCAATCCCGTTCCTGATCAGCA frameshift_variant 0.15
mmpL5 777976 p.Val169Ile missense_variant 0.29
mmpS5 778512 p.Asp132Asn missense_variant 0.33
mmpR5 779168 p.Leu60Gln missense_variant 0.4
mmpL5 779325 c.-845G>A upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781859 c.300T>A synonymous_variant 0.17
rplC 801247 p.Arg147Cys missense_variant 0.2
fbiC 1302774 c.-157A>G upstream_gene_variant 0.22
fbiC 1303607 p.Lys226Arg missense_variant 0.22
fbiC 1303665 c.735G>A synonymous_variant 0.15
fbiC 1305213 c.2283C>T synonymous_variant 0.12
fbiC 1305276 c.2346G>A synonymous_variant 0.14
Rv1258c 1406204 c.1137G>T synonymous_variant 0.22
Rv1258c 1406503 p.Val280Met missense_variant 0.14
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472205 n.360G>A non_coding_transcript_exon_variant 0.15
rrl 1474176 n.519A>T non_coding_transcript_exon_variant 0.17
rrl 1474182 n.525C>T non_coding_transcript_exon_variant 0.22
rrl 1474991 n.1334T>A non_coding_transcript_exon_variant 0.25
rrl 1476241 n.2584A>T non_coding_transcript_exon_variant 0.13
fabG1 1673313 c.-127T>C upstream_gene_variant 0.5
fabG1 1673329 c.-111A>G upstream_gene_variant 0.4
inhA 1674318 c.117C>G synonymous_variant 0.29
inhA 1674440 p.Glu80Val missense_variant 0.4
rpsA 1833922 p.Lys127Asn missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102766 p.Asp93Asn missense_variant 0.22
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154947 p.Ile389Val missense_variant 0.12
katG 2155719 c.393G>C synonymous_variant 0.4
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169530 p.Phe361Leu missense_variant 0.17
Rv1979c 2222149 p.Arg339His missense_variant 0.13
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223064 p.Leu34Gln missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288978 c.264G>A synonymous_variant 0.29
pncA 2290010 c.-769G>C upstream_gene_variant 0.33
pncA 2290215 c.-974C>T upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518324 c.210C>T synonymous_variant 0.22
kasA 2518535 p.Ala141Thr missense_variant 1.0
kasA 2518728 p.Leu205Gln missense_variant 0.33
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2747120 p.Phe160Ser missense_variant 0.29
folC 2747444 p.Ala52Glu missense_variant 0.4
folC 2747517 p.Leu28Met missense_variant 0.2
pepQ 2859441 c.978C>T synonymous_variant 0.22
pepQ 2859754 p.Phe222Tyr missense_variant 0.2
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065642 p.Asp184Asn missense_variant 0.29
thyA 3074532 c.-61C>A upstream_gene_variant 0.4
thyA 3074535 c.-64C>T upstream_gene_variant 0.33
ald 3086726 c.-94C>T upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087287 c.468C>T synonymous_variant 0.15
fbiD 3339123 c.6C>T synonymous_variant 0.17
Rv3083 3448439 c.-65G>A upstream_gene_variant 0.12
Rv3083 3448714 p.Asp71His missense_variant 1.0
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.192C>A synonymous_variant 0.17
Rv3236c 3612938 p.Thr60Ile missense_variant 0.29
alr 3840319 p.Pro368Ser missense_variant 0.18
alr 3841241 p.Gln60His missense_variant 0.18
alr 3841546 c.-126C>A upstream_gene_variant 0.24
ddn 3986970 p.Lys43Glu missense_variant 1.0
clpC1 4038274 p.Gly811Cys missense_variant 0.4
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239785 c.-78C>A upstream_gene_variant 0.14
embC 4240486 c.624G>A synonymous_variant 0.13
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241454 p.Ile531Asn missense_variant 0.25
embC 4241490 p.Ala543Val missense_variant 0.22
embC 4241527 c.1665C>T synonymous_variant 0.18
embC 4241614 c.1752A>G synonymous_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245245 c.2013C>A synonymous_variant 0.14
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247721 p.Arg403Gln missense_variant 0.25
embB 4247803 c.1290G>A synonymous_variant 0.29
embB 4247874 p.Ala454Gly missense_variant 0.25
embB 4248784 c.2271T>C synonymous_variant 0.17
aftB 4267229 p.Trp536* stop_gained 0.22
aftB 4268840 c.-4G>T upstream_gene_variant 0.15
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326372 p.Ala368Thr missense_variant 0.17
ethA 4327205 p.Ala90Val missense_variant 0.18
ethR 4327645 p.Ala33Thr missense_variant 0.18
ethR 4327723 p.Pro59Ser missense_variant 0.2
ethA 4327836 c.-363G>A upstream_gene_variant 1.0
ethA 4328390 c.-917G>T upstream_gene_variant 0.33
whiB6 4338441 p.Tyr27* stop_gained 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407711 c.492C>T synonymous_variant 0.5
gid 4407835 p.Trp123* stop_gained 0.67
gid 4407873 c.330G>T synonymous_variant 1.0