TB-Profiler result

Run: SRR5535698
Summary

Run ID: SRR5535698

Sample name:

Date: 04-04-2023 10:38:05

Number of reads: 1335720

Percentage reads mapped: 99.32

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 0.96
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8884 p.Arg528Leu missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9460 p.Gly720Val missense_variant 0.12
gyrA 9484 p.Ser728* stop_gained 0.14
fgd1 491591 p.Lys270Met missense_variant 1.0
fgd1 491604 c.822G>C synonymous_variant 0.12
fgd1 491780 p.Arg333Leu missense_variant 0.13
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576278 p.Gly311* stop_gained 0.14
mshA 576623 p.Ala426Ser missense_variant 0.13
mshA 576737 p.Val464Leu missense_variant 0.14
rpoB 759886 p.Pro27His missense_variant 0.22
rpoB 760019 c.213G>T synonymous_variant 0.14
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760492 p.Thr229Asn missense_variant 0.3
rpoB 761731 p.Gly642Val missense_variant 0.25
rpoB 761921 c.2115C>A synonymous_variant 0.15
rpoB 762224 c.2418C>T synonymous_variant 0.15
rpoB 762416 p.Lys870Asn missense_variant 0.25
rpoB 763219 p.Ala1138Glu missense_variant 0.25
rpoC 763565 p.Lys66* stop_gained 0.15
rpoC 763667 p.Pro100Thr missense_variant 0.2
rpoC 763762 c.393C>T synonymous_variant 0.25
rpoC 764170 p.Asn267Lys missense_variant 0.17
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765783 p.Ser805Tyr missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776384 c.2097C>A synonymous_variant 0.14
mmpL5 776832 p.Thr550Asn missense_variant 0.18
mmpL5 777542 c.939G>A synonymous_variant 0.17
mmpL5 777695 c.786G>T synonymous_variant 0.33
mmpL5 777882 p.Gly200Val missense_variant 0.14
mmpL5 778089 p.Gly131Val missense_variant 0.17
mmpL5 778278 p.Ala68Glu missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781609 p.Ser17Ile missense_variant 0.14
rplC 800786 c.-23C>A upstream_gene_variant 0.18
rplC 801258 c.450C>A synonymous_variant 0.2
fbiC 1302882 c.-49C>A upstream_gene_variant 0.12
fbiC 1303052 p.Val41Ala missense_variant 0.14
fbiC 1303737 p.Glu269Asp missense_variant 0.14
fbiC 1303739 p.Arg270Leu missense_variant 0.17
fbiC 1303839 p.Met303Ile missense_variant 0.29
Rv1258c 1406554 p.Ala263Ser missense_variant 0.18
Rv1258c 1406586 p.Thr252Asn missense_variant 0.14
Rv1258c 1407468 c.-128C>A upstream_gene_variant 0.25
Rv1258c 1407515 c.-175G>T upstream_gene_variant 0.14
embR 1416619 c.729C>A synonymous_variant 0.18
embR 1416920 p.Arg143Ile missense_variant 0.18
atpE 1461083 c.39T>C synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472153 n.308G>T non_coding_transcript_exon_variant 0.5
rrs 1472433 n.588G>T non_coding_transcript_exon_variant 1.0
fabG1 1673360 c.-80C>A upstream_gene_variant 0.2
fabG1 1673417 c.-23C>A upstream_gene_variant 0.12
fabG1 1673820 p.Met127Ile missense_variant 0.22
fabG1 1674068 p.Arg210Leu missense_variant 0.18
rpsA 1833507 c.-35C>A upstream_gene_variant 0.2
rpsA 1833929 p.Val130Phe missense_variant 0.18
rpsA 1834022 c.481C>T synonymous_variant 0.17
rpsA 1834594 c.1053C>A synonymous_variant 0.13
rpsA 1834608 p.Arg356Leu missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102195 p.Ser283Ile missense_variant 0.22
ndh 2102326 c.717G>T synonymous_variant 0.4
ndh 2102419 p.Lys208Asn missense_variant 0.18
ndh 2102535 p.Leu170Val missense_variant 0.25
ndh 2102559 p.Ser162Gly missense_variant 0.18
katG 2154207 c.1905C>A synonymous_variant 0.15
katG 2154514 p.Pro533Gln missense_variant 0.12
katG 2154808 p.Thr435Asn missense_variant 0.2
katG 2155608 c.504C>T synonymous_variant 0.22
PPE35 2168259 p.Thr785Met missense_variant 0.2
PPE35 2168437 p.Leu726Ile missense_variant 0.22
PPE35 2168712 p.Ala634Glu missense_variant 0.18
PPE35 2168852 c.1761G>T synonymous_variant 0.15
PPE35 2169278 c.1335T>C synonymous_variant 0.12
PPE35 2169281 c.1332T>G synonymous_variant 0.12
PPE35 2170173 c.437_439dupTGG conservative_inframe_insertion 1.0
PPE35 2170575 p.Ala13Asp missense_variant 0.15
Rv1979c 2222016 p.Phe383Leu missense_variant 0.14
Rv1979c 2222267 p.Phe300Val missense_variant 0.15
Rv1979c 2222787 c.378C>A synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289015 p.Thr76Asn missense_variant 0.13
pncA 2289433 c.-192C>A upstream_gene_variant 0.17
pncA 2289453 c.-212G>T upstream_gene_variant 0.18
pncA 2289720 c.-479C>T upstream_gene_variant 0.2
pncA 2289996 c.-755C>T upstream_gene_variant 0.12
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518103 c.-12G>T upstream_gene_variant 0.25
kasA 2519081 p.Ala323Thr missense_variant 0.4
eis 2714145 c.1188C>A synonymous_variant 0.25
eis 2714709 c.624C>A synonymous_variant 0.25
eis 2714861 c.472C>T synonymous_variant 0.18
ahpC 2726388 p.Ala66Thr missense_variant 0.17
folC 2747289 p.Pro104Ser missense_variant 0.12
folC 2747725 c.-127C>A upstream_gene_variant 0.17
pepQ 2859365 p.Pro352Thr missense_variant 0.13
pepQ 2859882 c.537G>T synonymous_variant 0.14
pepQ 2860256 p.Ala55Ser missense_variant 0.2
ribD 2987026 p.Ala63Asp missense_variant 0.2
ribD 2987389 p.Ala184Asp missense_variant 0.13
Rv2752c 3064858 p.Gly445Val missense_variant 0.14
Rv2752c 3064868 p.Val442Leu missense_variant 0.14
Rv2752c 3064895 p.Ala433Ser missense_variant 0.14
Rv2752c 3065247 p.Leu315Phe missense_variant 0.3
thyX 3068159 c.-214G>T upstream_gene_variant 0.18
thyA 3073705 p.Ala256Glu missense_variant 0.15
thyA 3073742 p.Glu244* stop_gained 0.18
thyA 3074124 c.348G>T synonymous_variant 0.4
thyA 3074190 p.Tyr94* stop_gained 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087685 p.Ala289Asp missense_variant 0.13
Rv3083 3449400 c.897C>T synonymous_variant 0.17
Rv3083 3449505 c.1002C>T synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474321 c.315C>A synonymous_variant 0.25
fprA 3474341 p.Leu112Ser missense_variant 0.22
fprA 3474351 c.345C>A synonymous_variant 0.18
fprA 3474936 c.930C>T synonymous_variant 0.2
fprA 3475042 p.Gly346Cys missense_variant 0.13
whiB7 3568802 c.-123G>T upstream_gene_variant 0.2
Rv3236c 3612281 p.Gly279Val missense_variant 0.13
Rv3236c 3613153 c.-37G>T upstream_gene_variant 0.15
Rv3236c 3613171 c.-55G>T upstream_gene_variant 0.15
fbiA 3640800 p.Trp86Cys missense_variant 0.1
fbiA 3641146 p.Ala202Ser missense_variant 0.22
fbiB 3641945 c.411C>G synonymous_variant 0.13
fbiB 3642215 c.681G>T synonymous_variant 0.2
fbiB 3642370 p.Ala279Val missense_variant 0.12
rpoA 3878061 c.447G>A synonymous_variant 0.29
rpoA 3878632 c.-125C>A upstream_gene_variant 1.0
clpC1 4038495 p.Arg737Gln missense_variant 0.18
clpC1 4039714 p.Tyr331His missense_variant 0.29
clpC1 4039802 c.903G>T synonymous_variant 0.29
clpC1 4040444 c.261C>T synonymous_variant 0.17
clpC1 4040541 p.Ser55Leu missense_variant 0.15
clpC1 4040709 c.-5C>G upstream_gene_variant 0.11
panD 4044171 p.Asp37Glu missense_variant 0.18
panD 4044311 c.-30G>T upstream_gene_variant 0.12
embC 4239877 c.15C>A synonymous_variant 0.18
embC 4240501 p.Ser213Arg missense_variant 0.13
embC 4241216 p.Ala452Ser missense_variant 0.18
embC 4241662 c.1800G>T synonymous_variant 0.25
embC 4242219 p.Thr786Lys missense_variant 0.15
embA 4242586 c.-647C>T upstream_gene_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242806 p.Phe982Ile missense_variant 1.0
embA 4242913 c.-320C>T upstream_gene_variant 0.13
embA 4243141 c.-92C>A upstream_gene_variant 0.22
embA 4243425 p.Gly65Trp missense_variant 0.14
embA 4243457 c.225C>A synonymous_variant 0.13
embA 4243779 p.Pro183Thr missense_variant 0.2
embA 4244028 p.Val266Ile missense_variant 0.2
embA 4245246 p.Gly672Trp missense_variant 0.25
embB 4245521 c.-993G>T upstream_gene_variant 0.5
embA 4245588 p.Val786Leu missense_variant 1.0
embB 4248265 p.Phe584Leu missense_variant 0.29
embB 4248304 c.1791G>T synonymous_variant 0.4
embB 4248592 c.2079C>A synonymous_variant 0.33
embB 4248719 c.2208_2210delCTG disruptive_inframe_deletion 0.22
embB 4248984 p.Pro824Arg missense_variant 0.1
embB 4249683 p.Trp1057Leu missense_variant 0.2
embB 4249701 p.Ser1063Tyr missense_variant 0.22
aftB 4267546 p.Asp431Tyr missense_variant 0.21
aftB 4268617 p.Gly74Ser missense_variant 0.33
ubiA 4269233 p.Arg201Ser missense_variant 0.15
ubiA 4269255 p.Tyr193* stop_gained 0.12
ethR 4326988 c.-561G>T upstream_gene_variant 0.17
ethA 4326996 p.Pro160Thr missense_variant 1.0
ethA 4327063 p.Cys137* stop_gained 0.2
whiB6 4338230 p.Leu98Met missense_variant 0.14
whiB6 4338288 c.234G>A synonymous_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407606 c.597C>T synonymous_variant 0.25
gid 4407634 p.Thr190Lys missense_variant 0.4
gid 4407948 p.Asp85Glu missense_variant 0.15
gid 4408218 c.-16G>T upstream_gene_variant 0.13
gid 4408258 c.-56C>T upstream_gene_variant 0.22
gid 4408471 c.-269G>T upstream_gene_variant 0.25