TB-Profiler result

Run: SRR21677892
Summary

Run ID: SRR21677892

Sample name:

Date: 04-04-2023 02:49:43

Number of reads: 542366

Percentage reads mapped: 98.62

Strain: lineage4.1.1.3

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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
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 6063 p.Ile275Asn missense_variant 0.12
gyrA 7210 c.-92C>T upstream_gene_variant 1.0
gyrA 7279 c.-23G>T upstream_gene_variant 0.12
gyrA 7346 c.45C>A synonymous_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7373 p.Met24Ile missense_variant 0.18
gyrA 7569 p.Ala90Ser missense_variant 0.13
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575712 p.Lys122Arg missense_variant 0.14
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776530 p.Gln651* stop_gained 0.14
mmpL5 776558 p.Met641Ile missense_variant 0.11
mmpL5 777393 p.Arg363Gln missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781435 c.-125G>C upstream_gene_variant 1.0
rplC 800815 c.7C>A synonymous_variant 0.13
rplC 800935 p.Glu43Lys missense_variant 0.25
fbiC 1304650 c.1722delC frameshift_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472030 n.185G>T non_coding_transcript_exon_variant 0.13
rrl 1473769 n.112T>A non_coding_transcript_exon_variant 0.17
rrl 1474450 n.793T>C non_coding_transcript_exon_variant 0.1
inhA 1673748 c.-454A>G upstream_gene_variant 0.11
fabG1 1673794 p.Val119Leu missense_variant 0.11
inhA 1674354 c.153C>A synonymous_variant 0.13
rpsA 1834232 p.Val231Leu missense_variant 0.11
rpsA 1834852 c.1311C>T synonymous_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918344 c.405C>T synonymous_variant 0.13
tlyA 1918397 p.Ala153Asp missense_variant 0.14
ndh 2102753 p.Gln97Arg missense_variant 0.1
PPE35 2170048 p.Leu189Val missense_variant 0.23
PPE35 2170053 p.Thr187Ser missense_variant 0.23
PPE35 2170066 p.Ala183Thr missense_variant 0.25
Rv1979c 2222051 p.Leu372Met missense_variant 0.11
Rv1979c 2222067 c.1098G>T synonymous_variant 0.11
Rv1979c 2222070 c.1095G>A synonymous_variant 0.12
Rv1979c 2222100 c.1065T>C synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288970 p.Glu91Gly missense_variant 0.11
pncA 2289761 c.-520A>G upstream_gene_variant 0.12
kasA 2518618 c.504G>A synonymous_variant 0.17
kasA 2519239 c.1125A>C synonymous_variant 0.14
eis 2714900 p.Arg145Cys missense_variant 0.15
eis 2715476 c.-144C>A upstream_gene_variant 0.12
folC 2746653 p.Gly316Ser missense_variant 0.2
folC 2747482 c.117G>A synonymous_variant 0.13
ribD 2987420 c.582C>G synonymous_variant 0.15
thyX 3067254 p.Glu231Gly missense_variant 0.11
thyX 3067510 p.Leu146Met missense_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339460 p.Gly115Ser missense_variant 0.18
fbiD 3339583 p.Thr156Pro missense_variant 0.13
Rv3083 3449183 p.Ser227Phe missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641051 c.511delG frameshift_variant 0.12
fbiB 3642519 p.Asp329Asn missense_variant 0.11
alr 3841073 c.348C>T synonymous_variant 0.11
ddn 3987166 p.Asp108Val missense_variant 0.14
embC 4241917 c.2056dupG frameshift_variant 0.12
embC 4242267 p.Arg802Leu missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244196 p.Val322Phe missense_variant 0.13
embA 4244860 p.Gly543Glu missense_variant 1.0
embB 4245908 c.-606G>A upstream_gene_variant 0.13
embA 4245945 p.Ile905Phe missense_variant 0.12
embB 4246817 p.Ala102Thr missense_variant 0.18
embB 4247606 c.1093C>T synonymous_variant 0.12
embB 4249117 c.2604G>A synonymous_variant 0.13
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4267938 p.Arg300Leu missense_variant 0.22
aftB 4268045 p.Tyr264* stop_gained 0.12
ubiA 4269696 c.137delA frameshift_variant 0.12
ethR 4328090 p.Arg181Leu missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 0.96