TB-Profiler result

Run: SRR4035813

Summary

Run ID: SRR4035813

Sample name:

Date: 04-04-2023 07:18:52

Number of reads: 1307468

Percentage reads mapped: 99.48

Strain: lineage4.1.2

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 0.99
lineage4.1.2 Euro-American T;H None 0.99
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 5180 c.-60T>C upstream_gene_variant 0.11
gyrB 6009 p.Leu257Pro missense_variant 0.11
gyrB 6148 c.909C>A synonymous_variant 0.15
gyrB 6533 p.Ala432Thr missense_variant 0.18
gyrA 7189 c.-113C>T upstream_gene_variant 0.13
gyrB 7194 p.Met652Thr missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7443 p.Leu48Val missense_variant 0.1
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 9208 p.Lys636Arg missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575502 p.Val52Glu missense_variant 0.17
mshA 575526 p.Pro60Gln missense_variant 0.14
mshA 575897 p.Lys184* stop_gained 0.17
mshA 576499 c.1152G>A synonymous_variant 0.14
ccsA 619945 p.Thr19Ala missense_variant 0.17
ccsA 620544 c.654G>A synonymous_variant 0.15
rpoB 759851 c.45G>A synonymous_variant 0.14
rpoB 759929 c.123A>T synonymous_variant 0.14
rpoB 759944 c.138A>T synonymous_variant 0.13
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761689 p.Ala628Val missense_variant 0.18
rpoB 762607 p.Ala934Val missense_variant 0.12
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764915 c.1546C>T synonymous_variant 0.14
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 778840 c.-360C>T upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303236 c.306C>T synonymous_variant 0.14
fbiC 1305355 p.Gly809Arg missense_variant 0.11
embR 1416679 c.669T>C synonymous_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472245 n.400C>T non_coding_transcript_exon_variant 0.29
rrs 1472534 n.689G>A non_coding_transcript_exon_variant 0.18
rrl 1474155 n.498G>T non_coding_transcript_exon_variant 0.13
rrl 1476283 n.2626A>G non_coding_transcript_exon_variant 0.12
rrl 1476525 n.2868A>T non_coding_transcript_exon_variant 0.14
fabG1 1673456 p.Thr6Ser missense_variant 0.12
fabG1 1673461 p.Gly8Arg missense_variant 0.12
fabG1 1673734 p.Arg99Gly missense_variant 0.12
rpsA 1833568 c.27G>C synonymous_variant 0.12
rpsA 1833862 c.321G>C synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918170 c.231C>T synonymous_variant 0.12
ndh 2102820 p.Val75Met missense_variant 0.18
katG 2155038 c.1074C>T synonymous_variant 0.13
PPE35 2169095 p.Leu506Phe missense_variant 0.12
PPE35 2169320 p.Leu431Phe missense_variant 0.19
PPE35 2170229 c.384A>G synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223325 c.-161G>C upstream_gene_variant 0.11
pncA 2289151 p.Ile31Val missense_variant 0.12
pncA 2289440 c.-199A>G upstream_gene_variant 0.12
pncA 2290110 c.-869C>T upstream_gene_variant 0.13
pncA 2290193 c.-952A>G upstream_gene_variant 0.15
pncA 2290200 c.-959A>G upstream_gene_variant 0.15
kasA 2517982 c.-133G>A upstream_gene_variant 0.13
kasA 2518076 c.-39C>T upstream_gene_variant 0.96
eis 2714991 c.342G>C synonymous_variant 0.12
eis 2715072 c.261G>A synonymous_variant 0.18
folC 2746368 p.Ala411Thr missense_variant 0.13
folC 2746388 p.Thr404Ile missense_variant 0.18
pepQ 2859463 p.Gly319Asp missense_variant 0.12
pepQ 2859566 c.852delC frameshift_variant 0.12
ribD 2987377 p.Ser180Phe missense_variant 0.15
Rv2752c 3064916 p.Gly426Ser missense_variant 0.13
thyX 3067650 p.Phe99Tyr missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087820 p.Arg334Leu missense_variant 0.13
Rv3083 3448636 p.Trp45Arg missense_variant 0.18
Rv3083 3448835 p.Ser111Asn missense_variant 0.13
Rv3083 3448842 c.339G>A synonymous_variant 0.13
Rv3083 3448847 p.Arg115His missense_variant 0.12
fprA 3473941 c.-66A>T upstream_gene_variant 0.13
fprA 3473950 c.-57G>C upstream_gene_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474000 c.-7C>T upstream_gene_variant 0.17
fprA 3474187 p.Lys61* stop_gained 0.14
fprA 3474194 p.Ile63Asn missense_variant 0.14
fprA 3474320 p.Gly105Asp missense_variant 0.12
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612540 p.Leu193Phe missense_variant 0.13
Rv3236c 3613001 p.Ala39Val missense_variant 0.22
Rv3236c 3613032 p.Ala29Thr missense_variant 0.15
fbiB 3642338 c.804C>G synonymous_variant 0.11
fbiB 3642821 c.1287C>A synonymous_variant 0.15
alr 3840779 c.642G>C synonymous_variant 0.11
alr 3841011 p.Gln137Pro missense_variant 0.11
alr 3841194 p.Arg76Leu missense_variant 0.15
alr 3841222 p.Ala67Thr missense_variant 0.15
rpoA 3878186 c.321delC frameshift_variant 0.11
clpC1 4038224 c.2481G>A synonymous_variant 0.13
clpC1 4040679 p.Ala9Val missense_variant 0.13
clpC1 4040686 p.Asp7Asn missense_variant 0.12
panD 4043906 p.Glu126Gln missense_variant 0.12
panD 4044381 c.-100C>G upstream_gene_variant 0.15
panD 4044399 c.-118C>A upstream_gene_variant 0.18
embC 4242163 c.2303delC frameshift_variant 0.12
embA 4242235 c.-998C>T upstream_gene_variant 0.13
embC 4242323 p.Gly821Cys missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243479 p.Pro83Ser missense_variant 0.12
embA 4245219 p.Trp663Gly missense_variant 0.13
embA 4245373 c.2142delG frameshift_variant 0.12
embA 4245931 p.Gly900Asp missense_variant 0.25
embA 4246089 p.Trp953Arg missense_variant 0.12
embB 4246535 p.Arg8Cys missense_variant 0.15
embB 4248993 p.Asn827Ser missense_variant 0.12
aftB 4267768 c.1069C>T synonymous_variant 0.27
ubiA 4269007 p.Asp276Val missense_variant 0.14
ubiA 4269337 p.Val166Ala missense_variant 0.12
ubiA 4269851 c.-18C>A upstream_gene_variant 0.15
whiB6 4338199 p.Asp108Gly missense_variant 0.18
whiB6 4338274 p.Glu83Val missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407531 c.672G>A synonymous_variant 0.14
gid 4408252 c.-50A>G upstream_gene_variant 0.15