TB-Profiler result

Run: SRR11972253
Summary

Run ID: SRR11972253

Sample name:

Date: 03-04-2023 05:33:38

Number of reads: 200545

Percentage reads mapped: 99.24

Strain: lineage1.1.3

Drug-resistance: MDR-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
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.94
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.9
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.22 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.82 isoniazid, ethionamide
embB 4247729 p.Gly406Ser missense_variant 1.0 ethambutol
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 5436 p.Asn66Ser missense_variant 0.6
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 7717 c.418delG frameshift_variant 0.67
gyrA 7734 p.Ile145Phe missense_variant 0.67
gyrA 8105 c.804G>A synonymous_variant 0.2
gyrA 8452 p.Ala384Val missense_variant 0.57
gyrA 8650 p.Arg450His missense_variant 0.4
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 0.3
rpoB 760160 c.354C>T synonymous_variant 0.4
rpoC 762611 c.-759C>T upstream_gene_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763440 p.Ser24Tyr missense_variant 0.2
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
rpoC 766616 c.3247C>A synonymous_variant 0.14
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778873 c.-393G>A upstream_gene_variant 0.25
mmpS5 779615 c.-710C>G upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781518 c.-42G>A upstream_gene_variant 0.29
rpsL 781884 p.Asn109Asp missense_variant 0.14
fbiC 1305123 p.Asp731Glu missense_variant 0.18
Rv1258c 1406782 p.Ala187Ser missense_variant 0.33
Rv1258c 1406867 c.474G>A synonymous_variant 0.33
embR 1417019 p.Cys110Tyr missense_variant 0.57
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474553 n.896T>C non_coding_transcript_exon_variant 0.36
rrl 1476618 n.2961C>T non_coding_transcript_exon_variant 0.17
fabG1 1673215 c.-225G>C upstream_gene_variant 0.64
ndh 2102148 p.Arg299Trp missense_variant 0.8
ndh 2102621 p.Ile141Asn missense_variant 0.4
katG 2154061 p.Ser684Ile missense_variant 0.22
katG 2154099 c.2013G>C synonymous_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155009 p.Phe368Tyr missense_variant 0.22
katG 2156490 c.-379G>A upstream_gene_variant 0.14
PPE35 2167745 p.Thr956Arg missense_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2168883 p.Gly577Asp missense_variant 0.25
PPE35 2169316 p.Asn433Asp missense_variant 0.17
PPE35 2169902 p.Leu237Phe missense_variant 0.56
PPE35 2169910 p.Asn235Tyr missense_variant 0.56
Rv1979c 2221836 c.1329T>C synonymous_variant 0.2
Rv1979c 2222671 p.Thr165Lys missense_variant 0.17
Rv1979c 2223184 c.-20T>C upstream_gene_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290065 c.-824G>A upstream_gene_variant 0.33
kasA 2518132 c.18C>T synonymous_variant 0.79
kasA 2519140 c.1026G>C synonymous_variant 0.14
kasA 2519143 c.1029G>C synonymous_variant 0.15
kasA 2519153 p.Ile347Val missense_variant 0.2
kasA 2519267 p.Val385Ile missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746429 c.1170C>T synonymous_variant 0.33
pepQ 2859324 c.1095C>T synonymous_variant 0.15
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065540 p.Val218Leu missense_variant 1.0
thyX 3067468 p.Ala160Thr missense_variant 0.67
thyA 3074341 p.Leu44Pro missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087148 p.Ser110Phe missense_variant 0.25
Rv3083 3449379 c.876G>A synonymous_variant 0.4
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
fprA 3475296 c.1290G>A synonymous_variant 0.29
whiB7 3568597 p.Trp28* stop_gained 0.2
fbiB 3641951 c.417G>A synonymous_variant 0.4
alr 3840917 c.504A>G synonymous_variant 0.2
alr 3841546 c.-126C>A upstream_gene_variant 0.22
alr 3841612 c.-193_-192insC upstream_gene_variant 0.15
rpoA 3877610 p.Lys300Glu missense_variant 0.22
rpoA 3878339 p.Asp57Asn missense_variant 0.83
rpoA 3878589 c.-82A>C upstream_gene_variant 0.33
ddn 3987194 c.351G>A synonymous_variant 0.13
clpC1 4038778 p.Glu643* stop_gained 0.33
clpC1 4039058 p.Phe549Leu missense_variant 0.5
clpC1 4040144 c.561G>C synonymous_variant 0.22
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040763 c.-59C>A upstream_gene_variant 0.13
panD 4044285 c.-4A>T upstream_gene_variant 0.25
embC 4240671 p.Thr270Ile missense_variant 0.89
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241748 p.Val629Glu missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244025 p.His265Tyr missense_variant 0.17
embA 4244061 p.Leu277Ile missense_variant 0.12
embA 4244628 p.Ile466Leu missense_variant 0.22
embA 4244857 p.Ala542Val missense_variant 0.18
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246137 p.Arg969Trp missense_variant 0.22
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249684 p.Trp1057* stop_gained 0.13
ubiA 4269387 p.Glu149Asp missense_variant 0.83
aftB 4269606 c.-770T>C upstream_gene_variant 0.44
ethA 4326794 p.Arg227His missense_variant 0.29
ethR 4327306 c.-243G>A upstream_gene_variant 0.33
whiB6 4338243 c.278delG frameshift_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 4407780 c.423G>A synonymous_variant 1.0
gid 4407835 p.Trp123* stop_gained 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4407973 p.Val77Gly missense_variant 0.25