TB-Profiler result

Run: SRR3732710
Summary

Run ID: SRR3732710

Sample name:

Date: 04-04-2023 05:38:24

Number of reads: 1489483

Percentage reads mapped: 99.73

Strain: lineage4.3.2

Drug-resistance: Sensitive

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.99
lineage4.3.2 Euro-American (LAM) LAM3 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 6175 p.Glu312Asp missense_variant 0.29
gyrB 6488 p.Arg417Ser missense_variant 0.33
gyrA 6496 c.-806G>A upstream_gene_variant 0.4
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7950 p.Ala217Ser missense_variant 0.4
gyrA 8323 p.Phe341Tyr missense_variant 0.2
gyrA 8700 p.Asp467Tyr missense_variant 0.17
gyrA 8769 p.His490Asn missense_variant 0.22
gyrA 8987 c.1686C>A synonymous_variant 0.13
gyrA 9226 p.Ser642Tyr missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490949 p.Ser56Phe missense_variant 0.22
fgd1 491027 p.Asn82Thr missense_variant 0.5
fgd1 491186 p.Ser135* stop_gained 0.15
mshA 575339 c.-9C>A upstream_gene_variant 0.17
ccsA 620107 p.Asp73Tyr missense_variant 0.17
rpoB 759710 c.-97C>A upstream_gene_variant 0.4
rpoB 759984 p.Gly60Ser missense_variant 0.22
rpoB 760397 p.Lys197Asn missense_variant 0.14
rpoB 760455 p.Gly217Ser missense_variant 0.17
rpoB 760783 p.Thr326Lys missense_variant 0.18
rpoB 760838 p.Glu344Asp missense_variant 0.22
rpoB 761647 p.Arg614His missense_variant 0.15
rpoB 762007 p.Arg734His missense_variant 0.17
rpoB 762285 p.Arg827Ser missense_variant 0.25
rpoB 762972 p.Gln1056Lys missense_variant 0.25
rpoB 763096 p.Tyr1097Cys missense_variant 0.18
rpoC 763950 p.Arg194Leu missense_variant 0.14
rpoC 764535 p.Arg389Leu missense_variant 0.18
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765302 p.Glu645* stop_gained 0.13
rpoC 766622 p.Arg1085Trp missense_variant 0.29
rpoC 767234 p.Glu1289* stop_gained 0.21
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775828 p.Gly885Trp missense_variant 0.2
mmpL5 775934 p.Asp849Glu missense_variant 0.18
mmpL5 776039 c.2442C>A synonymous_variant 0.5
mmpL5 776165 p.Asn772Lys missense_variant 0.17
mmpL5 777655 p.Asp276Tyr missense_variant 0.15
mmpL5 777983 c.498G>T synonymous_variant 0.18
mmpL5 778059 p.Ser141Ile missense_variant 0.15
mmpR5 778190 c.-800G>T upstream_gene_variant 0.15
mmpL5 778416 p.Pro22Gln missense_variant 0.25
mmpL5 778422 p.Ala20Glu missense_variant 0.25
mmpS5 779595 c.-690G>T upstream_gene_variant 0.33
mmpS5 779625 c.-720G>T upstream_gene_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781830 p.Pro91Thr missense_variant 0.17
rplC 801044 p.Arg79Leu missense_variant 0.33
fbiC 1302915 c.-16G>T upstream_gene_variant 0.33
fbiC 1303270 p.Leu114Ile missense_variant 0.25
fbiC 1303508 p.Pro193Gln missense_variant 0.57
fbiC 1303611 c.681G>T synonymous_variant 0.18
fbiC 1303743 c.813C>A synonymous_variant 0.22
fbiC 1303762 p.Arg278Ser missense_variant 0.4
fbiC 1304091 c.1161C>T synonymous_variant 1.0
fbiC 1304138 p.Ala403Val missense_variant 0.13
fbiC 1304626 p.Ala566Ser missense_variant 0.17
fbiC 1304653 p.Asp575Tyr missense_variant 0.14
fbiC 1304866 p.Gly646Trp missense_variant 0.22
Rv1258c 1406366 c.975C>T synonymous_variant 0.15
Rv1258c 1406372 c.969G>A synonymous_variant 0.17
embR 1416735 p.Glu205* stop_gained 0.18
atpE 1461078 p.Gly12Ser missense_variant 0.67
atpE 1461229 p.Ala62Glu missense_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473022 n.1177G>T non_coding_transcript_exon_variant 0.67
rrl 1475045 n.1388C>A non_coding_transcript_exon_variant 0.4
rrl 1475394 n.1737G>A non_coding_transcript_exon_variant 0.33
inhA 1673460 c.-742A>G upstream_gene_variant 0.33
inhA 1673839 c.-363C>A upstream_gene_variant 0.4
fabG1 1674118 p.Glu227* stop_gained 0.15
inhA 1674432 c.231G>T synonymous_variant 0.25
inhA 1674820 p.Leu207Ile missense_variant 0.14
rpsA 1833854 p.Lys105Glu missense_variant 0.22
rpsA 1833908 p.Asp123Tyr missense_variant 0.2
rpsA 1833970 c.429G>T synonymous_variant 0.29
rpsA 1834000 c.459G>T synonymous_variant 0.22
rpsA 1834100 p.Arg187Ser missense_variant 0.2
rpsA 1834513 c.972C>A synonymous_variant 0.4
rpsA 1834733 p.Ala398Thr missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918395 c.456G>A synonymous_variant 0.2
ndh 2101933 p.Met370Ile missense_variant 0.18
ndh 2102956 c.87G>T synonymous_variant 0.4
ndh 2103074 c.-32C>A upstream_gene_variant 0.33
katG 2153997 c.2115G>T synonymous_variant 0.18
katG 2154863 p.His417Asn missense_variant 0.15
katG 2154926 p.Arg396Cys missense_variant 0.18
katG 2154975 c.1137C>A synonymous_variant 0.18
PPE35 2167682 c.2931G>T synonymous_variant 0.25
PPE35 2167808 c.2805C>T synonymous_variant 0.25
PPE35 2168096 c.2517C>A synonymous_variant 0.22
PPE35 2169516 p.Ser366Tyr missense_variant 0.67
Rv1979c 2221842 c.1323G>T synonymous_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288835 p.Asp136Val missense_variant 0.14
pncA 2288963 c.279G>A synonymous_variant 0.14
pncA 2289480 c.-239G>T upstream_gene_variant 0.25
pncA 2290041 c.-800C>A upstream_gene_variant 0.15
kasA 2518058 c.-57G>T upstream_gene_variant 0.25
kasA 2518252 c.138C>A synonymous_variant 0.22
ahpC 2725933 c.-260G>T upstream_gene_variant 0.14
folC 2746959 p.Gly214Trp missense_variant 0.22
folC 2747158 c.441G>T synonymous_variant 0.22
pepQ 2859639 c.780T>A synonymous_variant 0.12
ribD 2986693 c.-146C>A upstream_gene_variant 0.25
ribD 2986850 c.12T>C synonymous_variant 0.17
ribD 2987041 p.Arg68Leu missense_variant 0.17
Rv2752c 3065756 p.Val146Ile missense_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3087645 p.Glu276Lys missense_variant 0.18
ald 3087726 p.Ala303Thr missense_variant 0.18
Rv3083 3448588 p.Asp29Tyr missense_variant 0.4
Rv3083 3448624 p.Leu41Met missense_variant 0.25
Rv3083 3448701 p.Phe66Leu missense_variant 0.18
Rv3083 3449013 c.510C>A synonymous_variant 0.2
Rv3083 3449315 p.Trp271Leu missense_variant 0.18
Rv3083 3449366 p.Pro288Gln missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474062 p.Ala19Glu missense_variant 0.2
fprA 3475005 c.999G>A synonymous_variant 0.33
fprA 3475215 c.1209C>A synonymous_variant 0.14
whiB7 3568471 c.207_208dupGA frameshift_variant 0.15
whiB7 3568761 c.-82G>T upstream_gene_variant 0.25
Rv3236c 3612180 p.Ala313Ser missense_variant 0.17
Rv3236c 3613030 c.87G>T synonymous_variant 0.29
Rv3236c 3613060 c.57G>T synonymous_variant 0.22
Rv3236c 3613274 c.-158C>T upstream_gene_variant 0.4
fbiA 3641332 p.Gly264Trp missense_variant 0.14
alr 3840289 p.Asp378Tyr missense_variant 0.15
alr 3840309 p.Arg371Leu missense_variant 0.25
alr 3841556 c.-136C>A upstream_gene_variant 0.15
alr 3841612 c.-193_-192insC upstream_gene_variant 1.0
ddn 3986745 c.-99A>C upstream_gene_variant 0.18
ddn 3986962 p.Thr40Asn missense_variant 0.22
ddn 3987161 c.318G>T synonymous_variant 0.18
clpC1 4038225 p.Pro827Gln missense_variant 0.18
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038656 p.Lys683Asn missense_variant 0.2
clpC1 4039071 p.Pro545Gln missense_variant 0.15
clpC1 4039145 p.Gly520Cys missense_variant 0.22
clpC1 4039277 c.1428C>T synonymous_variant 0.18
clpC1 4039359 p.Ser449Ile missense_variant 0.18
clpC1 4039362 p.Ala448Asp missense_variant 0.18
clpC1 4039365 p.Ala447Asp missense_variant 0.18
clpC1 4039372 p.Glu445* stop_gained 0.2
panD 4044211 p.Gly24Val missense_variant 0.22
embC 4239783 c.-80C>A upstream_gene_variant 0.15
embC 4240903 c.1041C>A synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244967 p.Gly579Trp missense_variant 0.18
embA 4245176 c.1944G>T synonymous_variant 0.17
embA 4245295 p.Thr688Lys missense_variant 0.22
embB 4245593 c.-921C>A upstream_gene_variant 0.29
embA 4245699 c.2469_2476delGTCGCACG frameshift_variant 0.18
embA 4246035 p.Glu935* stop_gained 0.18
embB 4246669 c.156C>A synonymous_variant 0.14
embB 4248857 p.Gly782* stop_gained 0.29
embB 4248930 p.Pro806His missense_variant 0.29
embB 4248959 p.Asp816Tyr missense_variant 0.22
embB 4249273 p.Asp920Glu missense_variant 0.22
aftB 4267607 p.Glu410Asp missense_variant 0.14
aftB 4268053 c.784C>A synonymous_variant 0.22
aftB 4268120 c.717C>A synonymous_variant 0.18
aftB 4268180 p.Phe219Leu missense_variant 0.18
aftB 4268250 p.Ala196Val missense_variant 0.18
ubiA 4269426 p.Leu136Phe missense_variant 0.25
ethA 4327060 p.Ser138Arg missense_variant 0.15
ethR 4327390 c.-159C>A upstream_gene_variant 0.5
whiB6 4338549 c.-28G>T upstream_gene_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407539 p.Gly222Trp missense_variant 0.18
gid 4407606 c.597C>A synonymous_variant 0.15
gid 4408156 p.Leu16Arg missense_variant 1.0