TB-Profiler result

Run: SRR19428557
Summary

Run ID: SRR19428557

Sample name:

Date: 03-04-2023 21:40:06

Number of reads: 349568

Percentage reads mapped: 99.73

Strain: lineage3.1

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
lineage3 East-African-Indian CAS RD750 0.06
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.27
lineage4.3.4 Euro-American (LAM) LAM RD174 0.81
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.73
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.77
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 2155388 c.723delC frameshift_variant 0.13 isoniazid
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 0.31
gyrB 6124 c.885C>T synonymous_variant 0.27
gyrB 6140 p.Val301Leu missense_variant 0.67
gyrB 6148 c.911delT frameshift_variant 0.11
gyrA 7168 c.-134C>T upstream_gene_variant 0.17
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 491226 c.444C>T synonymous_variant 0.12
fgd1 491383 c.602delA frameshift_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 0.18
mshA 575186 c.-161delG upstream_gene_variant 0.12
rpoB 759746 c.-61C>T upstream_gene_variant 0.17
rpoC 762434 c.-936T>G upstream_gene_variant 0.17
rpoB 762861 p.Val1019Phe missense_variant 0.17
rpoC 764995 c.1626C>G synonymous_variant 0.8
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775733 c.2747delT frameshift_variant 0.18
mmpL5 776100 p.Thr794Ile missense_variant 0.26
mmpL5 776182 p.Asp767Asn missense_variant 0.11
mmpL5 776674 p.Val603Met missense_variant 0.1
mmpL5 777905 c.576G>T synonymous_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781606 p.Ile16Thr missense_variant 0.12
rplC 801167 c.360delC frameshift_variant 0.18
fbiC 1302975 c.45C>A synonymous_variant 0.17
fbiC 1305413 p.Lys828Arg missense_variant 0.15
Rv1258c 1406349 p.Ile331Ser missense_variant 0.25
Rv1258c 1406724 c.616delC frameshift_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471984 n.139T>C non_coding_transcript_exon_variant 0.1
rrl 1475114 n.1457C>T non_coding_transcript_exon_variant 0.55
fabG1 1673283 c.-157A>C upstream_gene_variant 0.14
rpsA 1833702 p.Asp54Ala missense_variant 0.11
rpsA 1834411 c.870T>A synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918435 p.Ala166Thr missense_variant 0.22
katG 2154456 p.Ile552Met missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 0.39
PPE35 2167926 p.Leu896Ser missense_variant 0.12
Rv1979c 2222844 c.321G>A synonymous_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.67
eis 2715028 p.Ala102Val missense_variant 0.12
eis 2715201 c.131delG frameshift_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 0.27
pepQ 2860405 c.13dupC frameshift_variant 0.18
ribD 2987444 c.606C>T synonymous_variant 0.13
ribD 2987473 p.Cys212Tyr missense_variant 0.11
Rv2752c 3065323 p.Ala290Val missense_variant 0.11
Rv2752c 3065677 p.Lys172Arg missense_variant 0.18
thyX 3067853 c.93C>A synonymous_variant 0.13
thyA 3073868 p.Thr202Ala missense_variant 0.86
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087200 c.381A>T synonymous_variant 0.12
fbiD 3339099 c.-19A>T upstream_gene_variant 0.13
Rv3083 3449073 c.570C>T synonymous_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475198 p.Phe398Leu missense_variant 0.15
fprA 3475327 c.1324dupG frameshift_variant 0.2
whiB7 3568485 c.195T>C synonymous_variant 0.13
whiB7 3568501 c.178dupG frameshift_variant 0.12
Rv3236c 3612009 p.Ala370Thr missense_variant 0.87
Rv3236c 3612148 c.969G>A synonymous_variant 0.12
alr 3840719 c.702A>G synonymous_variant 0.6
alr 3841511 c.-91C>A upstream_gene_variant 0.1
clpC1 4038287 c.2418C>T synonymous_variant 0.7
clpC1 4039004 c.1701C>T synonymous_variant 0.13
clpC1 4040063 c.642G>A synonymous_variant 0.18
clpC1 4040704 c.1A>G start_lost 0.12
panD 4043938 p.Ile115Thr missense_variant 0.62
embC 4241726 p.Phe622Leu missense_variant 0.22
embC 4242075 p.Arg738Gln missense_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242904 p.Asp1014Glu missense_variant 0.2
embA 4243235 c.3G>A synonymous_variant 0.14
embA 4243345 p.Gln38Arg missense_variant 0.1
embA 4243367 c.137dupC frameshift_variant 0.12
embA 4245046 p.Leu605Pro missense_variant 0.12
embA 4245166 p.Pro645Gln missense_variant 0.21
embA 4245768 p.Asn846Asp missense_variant 0.29
embB 4247575 c.1062C>T synonymous_variant 0.1
embB 4247578 c.1065G>A synonymous_variant 0.1
embB 4247646 p.Glu378Ala missense_variant 0.1
embB 4249264 c.2754dupC frameshift_variant 0.18
aftB 4268276 c.561G>A synonymous_variant 0.15
aftB 4268899 c.-63G>T upstream_gene_variant 0.18
ubiA 4269073 p.Pro254Gln missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338718 c.-197C>T upstream_gene_variant 0.1
gid 4407588 c.615A>G synonymous_variant 0.25
gid 4408156 p.Leu16Arg missense_variant 0.56