TB-Profiler result

Run: SRR11535172
Summary

Run ID: SRR11535172

Sample name:

Date: 02-04-2023 21:39:39

Number of reads: 402325

Percentage reads mapped: 93.08

Strain: La1.8.1

Drug-resistance: Other

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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
La1 M.bovis None None 1.0
La1.8 M.bovis None None 1.0
La1.8.1 M.bovis None None 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
pncA 2289073 p.His57Asp missense_variant 1.0 pyrazinamide
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 5752 c.513G>A synonymous_variant 1.0
gyrA 6406 c.-896C>T upstream_gene_variant 1.0
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8285 c.984C>T synonymous_variant 1.0
gyrA 8505 p.Asp402Asn missense_variant 0.18
gyrA 8762 c.1461G>A synonymous_variant 0.2
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9217 p.Asp639Ala missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9660 p.Ala787Thr missense_variant 0.12
fgd1 490751 c.-32T>G upstream_gene_variant 0.3
fgd1 491125 p.Ala115Ser missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 761543 c.1737G>A synonymous_variant 0.25
rpoB 761848 c.2046delC frameshift_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763720 c.351G>C synonymous_variant 0.22
rpoC 764513 p.Phe382Leu missense_variant 0.17
rpoC 766352 p.Val995Ile missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302802 c.-129G>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1304260 c.1334delG frameshift_variant 0.22
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.67
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474320 n.663G>A non_coding_transcript_exon_variant 0.13
rrl 1474743 n.1086T>C non_coding_transcript_exon_variant 0.15
inhA 1674879 c.678T>C synonymous_variant 0.2
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102193 p.Arg284Trp missense_variant 1.0
ndh 2102922 p.Lys41Glu missense_variant 0.14
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154393 c.1719T>C synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154996 c.1116G>T synonymous_variant 0.15
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2155621 p.Leu164Gln missense_variant 0.12
katG 2156025 c.87C>A synonymous_variant 1.0
PPE35 2167873 p.Ser914Pro missense_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167960 p.Pro885Ser missense_variant 0.2
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168041 p.Ala858Ser missense_variant 0.12
PPE35 2168319 p.Thr765Ile missense_variant 1.0
PPE35 2168690 c.1923T>C synonymous_variant 0.15
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.53
PPE35 2170053 p.Thr187Ser missense_variant 0.53
Rv1979c 2222272 p.Ala298Gly missense_variant 0.1
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223350 c.-186T>G upstream_gene_variant 0.15
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715125 p.Thr70Ala missense_variant 1.0
folC 2746159 c.1440C>A synonymous_variant 0.17
folC 2747695 c.-97C>T upstream_gene_variant 0.25
pepQ 2859592 p.Ala276Glu missense_variant 0.18
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 1.0
ald 3087482 c.663G>A synonymous_variant 0.15
Rv3083 3448783 p.Val94Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiB 3641886 p.Leu118Ile missense_variant 0.2
alr 3840561 p.Ile287Asn missense_variant 0.12
alr 3841408 p.Trp5Arg missense_variant 0.12
rpoA 3878258 p.Val84Met missense_variant 0.15
rpoA 3878567 c.-60C>G upstream_gene_variant 0.67
clpC1 4038403 c.2302T>C synonymous_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240970 p.Ala370Thr missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242844 c.-389A>G upstream_gene_variant 0.12
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248711 p.Tyr733Cys missense_variant 0.11
aftB 4267418 c.1419G>A synonymous_variant 0.12
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326999 p.Gly159Arg missense_variant 0.17
ethR 4328083 p.Asn179Asp missense_variant 0.2
ethA 4328322 c.-849G>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407693 c.510A>G synonymous_variant 0.18