TB-Profiler result

Run: SRR4035834
Summary

Run ID: SRR4035834

Sample name:

Date: 04-04-2023 07:19:40

Number of reads: 1051269

Percentage reads mapped: 99.44

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H 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 2289026 p.Cys72Trp missense_variant 0.13 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
gyrA 7319 c.18G>A synonymous_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7448 p.Lys49Asn missense_variant 0.11
gyrA 7463 c.162G>C synonymous_variant 0.11
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7805 c.504C>T synonymous_variant 0.29
gyrA 7820 c.519G>A synonymous_variant 0.13
gyrA 7828 p.Asn176Ile missense_variant 0.13
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 8634 p.Ala445Ser missense_variant 0.12
gyrA 8862 p.Thr521Ala missense_variant 0.14
gyrA 9033 p.Arg578Trp missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9388 p.Ala696Gly missense_variant 0.1
gyrA 9453 p.Arg718Ser missense_variant 0.12
fgd1 490592 c.-191C>A upstream_gene_variant 0.17
fgd1 491518 p.Thr246Ala missense_variant 0.22
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575504 p.His53Tyr missense_variant 0.22
ccsA 620017 p.Gly43Arg missense_variant 0.13
ccsA 620359 p.Tyr157His missense_variant 0.11
ccsA 620630 p.Gly247Asp missense_variant 0.15
rpoB 760017 c.211C>A synonymous_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760747 p.Leu314His missense_variant 0.2
rpoB 760758 p.Val318Ile missense_variant 0.15
rpoB 760770 p.Ile322Val missense_variant 0.13
rpoB 760783 p.Thr326Lys missense_variant 0.15
rpoC 763103 c.-267G>T upstream_gene_variant 0.13
rpoC 763899 p.Leu177Pro missense_variant 0.22
rpoC 763974 p.Glu202Gly missense_variant 0.12
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764811 p.Pro481Arg missense_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765228 p.Met620Lys missense_variant 0.14
rpoC 765275 p.Arg636Trp missense_variant 0.2
rpoC 765866 p.Pro833Thr missense_variant 0.14
rpoC 766488 p.Pro1040Leu missense_variant 0.15
rpoC 766779 p.Glu1137Gly missense_variant 0.11
rpoC 766899 p.Pro1177Leu missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776205 p.Gly759Val missense_variant 0.22
mmpL5 776339 p.His714Gln missense_variant 0.12
mmpL5 777083 c.1398C>T synonymous_variant 0.15
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 777922 p.Thr187Ala missense_variant 0.11
mmpS5 778554 p.Val118Ile missense_variant 0.15
mmpS5 778704 p.Asn68Asp missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304320 p.Ser464Cys missense_variant 0.25
fbiC 1304338 p.Phe470Leu missense_variant 0.18
fbiC 1304404 p.Asp492His missense_variant 0.2
Rv1258c 1406810 c.531C>A synonymous_variant 0.25
Rv1258c 1407028 p.Val105Leu missense_variant 0.15
Rv1258c 1407430 c.-90A>G upstream_gene_variant 0.14
embR 1416434 p.Ala305Val missense_variant 0.13
embR 1416438 p.Gln304* stop_gained 0.12
atpE 1460858 c.-187C>A upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473802 n.145C>G non_coding_transcript_exon_variant 0.11
rrl 1474492 n.839_840delCG non_coding_transcript_exon_variant 0.15
rrl 1475200 n.1543T>G non_coding_transcript_exon_variant 0.12
rrl 1476045 n.2388G>T non_coding_transcript_exon_variant 0.12
fabG1 1673714 p.Ser92Phe missense_variant 0.14
fabG1 1674181 c.742T>C stop_lost&splice_region_variant 0.12
inhA 1674711 c.510G>C synonymous_variant 0.12
inhA 1674720 p.Arg173Ser missense_variant 0.11
inhA 1674756 c.555T>C synonymous_variant 0.12
rpsA 1833380 c.-162G>A upstream_gene_variant 0.18
rpsA 1833463 c.-79C>A upstream_gene_variant 0.22
rpsA 1834829 p.Ala430Pro missense_variant 0.12
rpsA 1834853 p.Ala438Thr missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918177 p.Ala80Thr missense_variant 0.19
tlyA 1918183 p.Ala82Ser missense_variant 0.12
tlyA 1918248 c.309T>G synonymous_variant 0.12
ndh 2102729 p.Gly105Ala missense_variant 0.17
katG 2153966 p.Ala716Ser missense_variant 0.18
katG 2154141 c.1971C>T synonymous_variant 0.14
katG 2155922 p.Tyr64His missense_variant 0.13
PPE35 2169918 c.694dupC frameshift_variant 0.15
PPE35 2170467 p.Thr49Lys missense_variant 0.14
Rv1979c 2221986 c.1179C>T synonymous_variant 0.13
Rv1979c 2222814 c.351G>C synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289389 c.-148A>T upstream_gene_variant 0.15
pncA 2289532 c.-291T>A upstream_gene_variant 0.14
pncA 2289551 c.-310C>T upstream_gene_variant 0.14
pncA 2289824 c.-583T>C upstream_gene_variant 0.15
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714707 p.Gly209Asp missense_variant 0.12
folC 2747146 p.Lys151Asn missense_variant 0.13
folC 2747692 c.-94A>G upstream_gene_variant 0.18
pepQ 2859332 p.Thr363Ala missense_variant 0.14
pepQ 2859767 p.Val218Met missense_variant 0.15
pepQ 2859980 p.Cys147Arg missense_variant 0.14
pepQ 2859989 p.Arg144* stop_gained 0.15
pepQ 2860403 p.Arg6Cys missense_variant 0.14
ribD 2987253 p.Ala139Thr missense_variant 0.25
ribD 2987604 p.Val256Ile missense_variant 0.18
Rv2752c 3065310 c.882G>A synonymous_variant 0.12
Rv2752c 3065817 c.375C>T synonymous_variant 0.2
Rv2752c 3066269 c.-78A>G upstream_gene_variant 0.12
thyA 3074652 c.-181T>A upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339255 c.138G>A synonymous_variant 0.13
fbiD 3339368 p.Thr84Ile missense_variant 0.13
Rv3083 3448640 p.Asp46Gly missense_variant 0.12
Rv3083 3448957 p.Asp152Asn missense_variant 0.14
Rv3083 3448984 p.Gly161Ser missense_variant 0.17
fprA 3473947 c.-60G>T upstream_gene_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474831 c.825G>T synonymous_variant 0.15
fprA 3475267 p.Ala421Thr missense_variant 0.12
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612147 p.Leu324Val missense_variant 0.2
Rv3236c 3612576 p.Ala181Ser missense_variant 0.13
fbiB 3641664 p.Asp44Asn missense_variant 0.14
fbiB 3642668 c.1134A>G synonymous_variant 0.12
alr 3840857 c.564C>G synonymous_variant 0.11
ddn 3986782 c.-62G>A upstream_gene_variant 0.15
ddn 3986795 c.-49C>T upstream_gene_variant 0.14
ddn 3986826 c.-18G>T upstream_gene_variant 0.13
ddn 3986850 p.Lys3Glu missense_variant 0.12
clpC1 4039927 p.Arg260Ser missense_variant 0.13
clpC1 4040416 p.Gln97* stop_gained 0.13
embC 4240396 c.534G>A synonymous_variant 0.15
embC 4240411 c.549G>A synonymous_variant 0.13
embC 4241157 p.Gly432Val missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244051 p.Asp273Glu missense_variant 0.14
embA 4244056 p.Gly275Ala missense_variant 0.15
embA 4244679 p.Ala483Pro missense_variant 0.13
embA 4244904 p.Val558Leu missense_variant 0.18
embA 4244947 p.Val572Ala missense_variant 0.13
embA 4246101 p.Thr957Pro missense_variant 0.25
embB 4247220 p.Leu236Ser missense_variant 0.17
embB 4247353 c.840C>T synonymous_variant 0.17
embB 4248209 p.Val566Met missense_variant 0.12
embB 4249047 p.Ala845Val missense_variant 0.13
aftB 4268277 p.Pro187Arg missense_variant 0.11
aftB 4268550 p.Val96Glu missense_variant 0.17
ubiA 4268986 c.847dupG frameshift_variant 0.18
ubiA 4269140 p.Cys232Arg missense_variant 0.11
ubiA 4269334 p.Ala167Asp missense_variant 0.15
ubiA 4269875 c.-42G>A upstream_gene_variant 0.18
ubiA 4269991 c.-158C>T upstream_gene_variant 0.2
ethA 4326852 p.Ser208Pro missense_variant 0.11
ethA 4327071 p.Phe135Leu missense_variant 0.12
ethA 4327422 p.Ser18Gly missense_variant 0.18
ethR 4327429 c.-120G>T upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338635 c.-114A>G upstream_gene_variant 0.12