TB-Profiler result

Run: SRR4034724

Summary

Run ID: SRR4034724

Sample name:

Date: 04-04-2023 07:00:26

Number of reads: 1503329

Percentage reads mapped: 95.84

Strain: lineage4.9

Drug-resistance: Other


Download CSV Download TXT Download PDF Download JSON
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
lineage4.9 Euro-American (H37Rv-like) T1 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 2289121 p.Tyr41His missense_variant 0.12 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 5605 c.366C>A synonymous_variant 0.15
gyrB 5903 p.Val222Met missense_variant 0.13
gyrA 6385 c.-917G>T upstream_gene_variant 0.12
gyrA 6535 c.-767C>A upstream_gene_variant 0.15
gyrB 6582 p.Thr448Met missense_variant 0.13
gyrB 7238 p.Ala667Thr missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9116 p.Glu605Asp missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 0.15
gyrA 9599 p.Leu766Phe missense_variant 0.17
fgd1 491172 c.390C>A synonymous_variant 0.15
mshA 575875 c.528C>A synonymous_variant 0.15
ccsA 619828 c.-63G>T upstream_gene_variant 0.15
ccsA 620052 c.162G>T synonymous_variant 0.23
ccsA 620566 p.Asp226Tyr missense_variant 0.17
rpoB 760582 p.Asp259Gly missense_variant 0.22
rpoB 760985 c.1179G>T synonymous_variant 0.22
rpoB 761474 c.1671_1677delCAAGGCG frameshift_variant 0.11
rpoB 761963 c.2157G>A synonymous_variant 0.13
rpoC 763804 c.435C>T synonymous_variant 0.13
rpoC 764807 p.Arg480Cys missense_variant 0.13
rpoC 766749 p.Pro1127His missense_variant 0.18
mmpL5 776291 c.2190G>T synonymous_variant 0.15
mmpL5 777695 c.786G>A synonymous_variant 0.17
mmpL5 778392 p.Thr30Ile missense_variant 0.17
mmpR5 778409 c.-581G>A upstream_gene_variant 0.15
mmpL5 778459 p.Ala8Thr missense_variant 0.14
mmpL5 779244 c.-764G>A upstream_gene_variant 0.14
mmpL5 779379 c.-899C>A upstream_gene_variant 0.13
rplC 801360 p.Lys184Asn missense_variant 0.13
rplC 801382 c.574C>T synonymous_variant 0.14
rplC 801441 c.633G>A synonymous_variant 0.18
Rv1258c 1406681 p.Trp220* stop_gained 0.15
embR 1417039 c.309C>A synonymous_variant 0.12
embR 1417245 p.Gln35Lys missense_variant 0.12
embR 1417269 p.Pro27Thr missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472017 n.172C>A non_coding_transcript_exon_variant 0.33
rrs 1472907 n.1062C>T non_coding_transcript_exon_variant 0.67
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 1.0
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 1.0
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.67
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.67
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.5
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.5
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.5
rpsA 1833347 c.-195T>C upstream_gene_variant 0.14
rpsA 1833434 c.-108C>G upstream_gene_variant 0.13
rpsA 1834414 c.873C>T synonymous_variant 0.22
rpsA 1834559 p.Val340Ile missense_variant 0.14
rpsA 1834893 p.Ala451Asp missense_variant 0.14
tlyA 1917852 c.-88G>A upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101990 c.1053G>T synonymous_variant 0.14
ndh 2102508 p.Gly179Ser missense_variant 0.17
katG 2154161 p.Glu651* stop_gained 0.13
katG 2154564 p.Lys516Asn missense_variant 0.13
katG 2154584 p.Pro510Thr missense_variant 0.13
katG 2154597 p.Trp505Cys missense_variant 0.12
katG 2155403 p.Gly237Cys missense_variant 0.13
katG 2155659 c.453C>T synonymous_variant 0.15
katG 2155679 p.Arg145Cys missense_variant 0.15
katG 2156388 c.-277G>T upstream_gene_variant 0.14
PPE35 2167742 c.2871C>A synonymous_variant 0.25
PPE35 2169266 c.1347C>T synonymous_variant 0.13
pncA 2289751 c.-510C>A upstream_gene_variant 0.29
eis 2714504 p.His277Asn missense_variant 0.12
eis 2715331 p.Val1Ala missense_variant 0.1
pepQ 2859518 p.Gln301* stop_gained 0.17
pepQ 2860148 p.Gly91Cys missense_variant 0.15
ribD 2986729 c.-110G>A upstream_gene_variant 0.22
Rv2752c 3064922 p.Glu424Lys missense_variant 0.14
Rv2752c 3065808 c.384C>T synonymous_variant 0.12
Rv2752c 3065976 c.216C>T synonymous_variant 0.14
Rv2752c 3067023 c.-832G>T upstream_gene_variant 0.14
thyX 3067525 p.Ala141Ser missense_variant 0.25
ald 3087372 p.Arg185Ser missense_variant 0.17
Rv3083 3448328 c.-176G>A upstream_gene_variant 0.13
Rv3083 3448486 c.-18C>A upstream_gene_variant 0.12
Rv3083 3449490 c.987C>A synonymous_variant 0.18
fprA 3474301 p.Ala99Ser missense_variant 0.22
Rv3236c 3612277 c.840G>A synonymous_variant 0.14
Rv3236c 3612343 c.774G>T synonymous_variant 0.17
Rv3236c 3612796 c.321G>T synonymous_variant 0.2
fbiA 3640476 c.-67C>G upstream_gene_variant 0.11
alr 3840498 p.Ala308Glu missense_variant 0.12
rpoA 3877851 p.Phe219Leu missense_variant 0.14
clpC1 4039191 p.Thr505Ile missense_variant 0.22
clpC1 4040146 c.559C>T synonymous_variant 0.12
clpC1 4040154 p.Glu184Gly missense_variant 0.14
panD 4044056 p.Ala76Thr missense_variant 0.17
embC 4240930 p.Trp356Cys missense_variant 0.15
embC 4240988 p.Ala376Thr missense_variant 0.2
embA 4242346 c.-887C>T upstream_gene_variant 0.2
embA 4243460 c.228C>T synonymous_variant 0.14
embA 4243899 p.Ala223Thr missense_variant 0.2
embA 4244285 c.1053G>A synonymous_variant 0.13
embA 4244329 p.Ala366Val missense_variant 0.12
embA 4244657 c.1425G>A synonymous_variant 0.12
embA 4246512 p.Pro1094Ser missense_variant 0.2
embB 4246705 c.192G>T synonymous_variant 0.2
embB 4247292 p.Ser260Leu missense_variant 0.13
embB 4248882 p.Pro790Leu missense_variant 0.14
aftB 4267306 p.Val511Ile missense_variant 0.12
aftB 4267705 p.Leu378Ile missense_variant 0.13
ubiA 4269020 p.Gly272Arg missense_variant 0.17
ubiA 4269259 p.Arg192His missense_variant 0.2
aftB 4269351 c.-515C>A upstream_gene_variant 0.15
ethA 4326436 c.1038G>A synonymous_variant 0.13
ethR 4327438 c.-111A>G upstream_gene_variant 0.14
ethA 4328461 c.-988C>T upstream_gene_variant 0.14
whiB6 4338184 p.Ala113Val missense_variant 0.13
whiB6 4338419 p.Thr35Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0