TB-Profiler result

Run: SRR5535697
Summary

Run ID: SRR5535697

Sample name:

Date: 04-04-2023 10:38:02

Number of reads: 1469171

Percentage reads mapped: 99.19

Strain: lineage4.1.2

Drug-resistance: HR-TB

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 0.99
lineage4.1.2 Euro-American T;H None 0.97
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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155666 p.Trp149* stop_gained 0.25 isoniazid
embC 4240676 p.Gly272Ser missense_variant 0.18 ethambutol
ethA 4326278 p.Ser399* stop_gained 1.0 ethionamide
gid 4407686 p.Glu173* stop_gained 0.29 streptomycin
gid 4407985 p.Gly73Ala missense_variant 1.0 streptomycin
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 5698 c.459G>T synonymous_variant 0.33
gyrB 5797 c.558C>T synonymous_variant 0.18
gyrB 6470 p.Val411Leu missense_variant 0.2
gyrB 6539 p.Asp434Tyr missense_variant 0.22
gyrB 7031 p.Gly598Trp missense_variant 0.67
gyrB 7127 p.Val630Phe missense_variant 0.5
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7802 c.501C>A synonymous_variant 0.18
gyrA 7818 p.Leu173Met missense_variant 0.14
gyrA 8223 p.Asp308Asn missense_variant 0.18
gyrA 8675 c.1374C>A synonymous_variant 0.2
gyrA 9239 c.1938C>T synonymous_variant 0.33
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9684 p.Gly795* stop_gained 0.5
fgd1 491522 p.Arg247Gln missense_variant 0.33
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575350 c.3G>T start_lost 0.38
mshA 575421 p.Thr25Asn missense_variant 0.14
mshA 575431 c.84C>A synonymous_variant 0.15
mshA 575449 c.102C>A synonymous_variant 0.17
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 575728 c.381C>A synonymous_variant 0.22
mshA 575743 p.Phe132Leu missense_variant 0.29
mshA 575821 c.474G>C synonymous_variant 0.15
mshA 576308 p.Ile321Val missense_variant 0.2
mshA 576318 p.Arg324Leu missense_variant 0.2
mshA 576776 p.Gly477Arg missense_variant 0.2
ccsA 619713 c.-178C>A upstream_gene_variant 0.17
ccsA 619716 c.-175G>T upstream_gene_variant 0.27
ccsA 619723 c.-168G>T upstream_gene_variant 0.18
ccsA 619724 c.-167C>A upstream_gene_variant 0.18
ccsA 619756 c.-135G>A upstream_gene_variant 0.2
ccsA 620323 p.Val145Met missense_variant 0.67
rpoB 759742 c.-65G>T upstream_gene_variant 0.4
rpoB 760520 c.714C>A synonymous_variant 0.25
rpoB 760536 p.Glu244* stop_gained 0.2
rpoB 760539 p.Arg245Trp missense_variant 0.2
rpoB 760564 p.Arg253Leu missense_variant 0.25
rpoB 760569 p.Thr255Pro missense_variant 0.25
rpoB 760688 p.Phe294Leu missense_variant 0.33
rpoB 760697 p.Glu297Asp missense_variant 0.33
rpoB 761000 p.Met398Ile missense_variant 0.5
rpoB 761298 p.Ala498Thr missense_variant 0.4
rpoB 761338 p.Arg511His missense_variant 0.4
rpoB 761610 p.Gly602Trp missense_variant 0.4
rpoB 761613 p.Ala603Ser missense_variant 0.4
rpoB 762831 p.Ser1009Arg missense_variant 0.4
rpoC 763187 c.-183C>A upstream_gene_variant 0.67
rpoC 763582 p.Lys71Asn missense_variant 0.25
rpoC 764057 p.Ala230Ser missense_variant 0.25
rpoC 764810 p.Pro481Thr missense_variant 0.27
rpoC 765150 p.Gly594Glu missense_variant 0.9
rpoC 765291 p.Arg641Leu missense_variant 0.25
rpoC 765402 p.Pro678Gln missense_variant 0.25
rpoC 765450 p.Ala694Asp missense_variant 0.25
rpoC 765544 c.2175C>A synonymous_variant 0.22
rpoC 765564 p.Ser732* stop_gained 0.25
rpoC 765572 p.Asp735Tyr missense_variant 0.25
rpoC 765598 p.Lys743Asn missense_variant 0.5
rpoC 765638 p.Glu757Lys missense_variant 0.29
rpoC 765664 p.Leu765Phe missense_variant 0.29
rpoC 765849 p.Pro827Gln missense_variant 0.17
rpoC 765932 p.Gly855Cys missense_variant 0.25
rpoC 766617 p.Arg1083Leu missense_variant 0.67
rpoC 767149 c.3780C>T synonymous_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775674 p.Trp936Leu missense_variant 0.17
mmpL5 775716 p.Arg922Gln missense_variant 0.25
mmpL5 775973 c.2508G>A synonymous_variant 1.0
mmpL5 776169 p.Gly771Val missense_variant 0.5
mmpL5 776759 p.Phe574Leu missense_variant 0.5
mmpL5 777310 p.Gly391Cys missense_variant 0.25
mmpL5 777319 p.Arg388Ser missense_variant 0.2
mmpS5 778484 p.Ser141Tyr missense_variant 0.18
mmpL5 778585 c.-105C>T upstream_gene_variant 0.22
mmpS5 778857 p.Val17Met missense_variant 0.4
mmpR5 779254 p.Arg89Trp missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781406 c.-154G>T upstream_gene_variant 0.33
rplC 800689 c.-120G>A upstream_gene_variant 0.25
rplC 800860 p.Asp18Asn missense_variant 0.18
rplC 800922 c.114C>A synonymous_variant 0.18
rplC 801078 c.270T>C synonymous_variant 0.13
fbiC 1302766 c.-165C>A upstream_gene_variant 0.22
fbiC 1303452 c.522G>T synonymous_variant 0.18
fbiC 1303690 p.Pro254Thr missense_variant 0.67
fbiC 1304800 p.Arg624Trp missense_variant 0.67
fbiC 1304862 p.Lys644Asn missense_variant 0.4
fbiC 1305152 p.Pro741Gln missense_variant 0.2
fbiC 1305265 p.Gly779Arg missense_variant 0.22
fbiC 1305463 p.Arg845Ser missense_variant 0.15
Rv1258c 1406120 c.1221C>A synonymous_variant 0.17
Rv1258c 1406294 c.1047C>A synonymous_variant 0.2
Rv1258c 1407426 c.-86C>A upstream_gene_variant 0.29
embR 1416253 c.1095C>T synonymous_variant 0.22
embR 1416369 p.Arg327Ser missense_variant 0.3
embR 1416435 p.Ala305Ser missense_variant 0.18
embR 1416718 p.Gln210His missense_variant 0.18
embR 1417031 p.Pro106His missense_variant 0.5
embR 1417194 p.Val52Phe missense_variant 0.4
rrs 1471771 n.-75C>A upstream_gene_variant 1.0
rrs 1473090 n.1245G>T non_coding_transcript_exon_variant 1.0
rrl 1473404 n.-254C>A upstream_gene_variant 0.4
rrl 1474503 n.846G>T non_coding_transcript_exon_variant 0.67
rrl 1475313 n.1656G>T non_coding_transcript_exon_variant 0.67
rrl 1476276 n.2619C>A non_coding_transcript_exon_variant 0.67
rrl 1476427 n.2770G>T non_coding_transcript_exon_variant 0.25
rrl 1476781 n.3124C>T non_coding_transcript_exon_variant 0.5
rrl 1476787 n.3130C>A non_coding_transcript_exon_variant 0.5
fabG1 1673912 p.Ala158Val missense_variant 0.5
fabG1 1674085 p.Glu216* stop_gained 0.67
fabG1 1674155 c.719_721delACG disruptive_inframe_deletion 0.4
inhA 1674312 c.111G>A synonymous_variant 0.29
inhA 1674329 p.Arg43Leu missense_variant 0.29
inhA 1674423 p.Leu74Phe missense_variant 0.33
inhA 1674775 p.Gly192Cys missense_variant 0.25
inhA 1674954 c.753G>A synonymous_variant 0.22
rpsA 1833775 p.Glu78Asp missense_variant 0.29
rpsA 1834093 c.552G>T synonymous_variant 0.2
rpsA 1834466 p.Ala309Ser missense_variant 0.6
rpsA 1834519 c.978G>T synonymous_variant 0.22
rpsA 1834876 c.1335G>T synonymous_variant 0.25
tlyA 1917792 c.-148G>T upstream_gene_variant 0.2
tlyA 1917800 c.-140A>C upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918387 p.Leu150Met missense_variant 0.17
tlyA 1918737 p.Glu266Asp missense_variant 0.29
tlyA 1918742 p.Pro268Gln missense_variant 0.29
ndh 2101942 p.Lys367Asn missense_variant 0.22
ndh 2101965 p.Glu360* stop_gained 0.25
ndh 2101975 c.1068G>T synonymous_variant 0.22
ndh 2102244 p.Arg267Trp missense_variant 0.22
ndh 2102813 p.Arg77His missense_variant 0.25
katG 2153907 c.2205C>T synonymous_variant 0.22
katG 2154035 p.Arg693Ser missense_variant 0.29
katG 2154183 c.1929G>T synonymous_variant 0.33
katG 2154584 p.Pro510Thr missense_variant 0.15
katG 2154910 p.Pro401His missense_variant 0.22
katG 2154933 c.1179C>A synonymous_variant 0.25
katG 2155020 c.1092C>T synonymous_variant 0.2
katG 2155030 p.Ala361Val missense_variant 0.25
katG 2155259 p.Gly285Cys missense_variant 0.67
katG 2155572 c.540G>A synonymous_variant 0.29
katG 2156469 c.-358G>T upstream_gene_variant 0.25
PPE35 2167910 c.2703C>A synonymous_variant 0.29
PPE35 2168917 p.Pro566Thr missense_variant 0.33
PPE35 2170073 p.Ala180Ser missense_variant 0.2
PPE35 2170132 p.Val161Ile missense_variant 0.25
PPE35 2170139 c.474G>A synonymous_variant 0.25
PPE35 2170147 p.Ser156Ala missense_variant 0.22
PPE35 2170157 p.Ala152Ser missense_variant 0.2
PPE35 2170222 p.Pro131Thr missense_variant 0.18
PPE35 2170319 p.Glu98Asp missense_variant 0.2
PPE35 2170628 c.-16C>A upstream_gene_variant 0.67
PPE35 2170761 c.-149G>T upstream_gene_variant 0.5
Rv1979c 2222085 c.1080G>A synonymous_variant 0.29
Rv1979c 2222155 p.Pro337Gln missense_variant 0.22
Rv1979c 2222451 c.714C>A synonymous_variant 0.33
Rv1979c 2222501 p.Ala222Thr missense_variant 1.0
Rv1979c 2222519 p.Gly216Cys missense_variant 0.29
Rv1979c 2223156 c.9C>A synonymous_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223297 c.-133G>T upstream_gene_variant 0.4
pncA 2289134 c.108C>A synonymous_variant 0.29
pncA 2289873 c.-632C>A upstream_gene_variant 0.4
pncA 2290021 c.-780C>A upstream_gene_variant 0.33
pncA 2290147 c.-906T>C upstream_gene_variant 0.5
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518152 p.Ser13Ile missense_variant 0.22
kasA 2518438 p.Phe108Leu missense_variant 0.22
kasA 2518530 p.Pro139Gln missense_variant 0.29
kasA 2518832 p.Gly240Cys missense_variant 0.18
kasA 2518849 c.735G>T synonymous_variant 0.25
kasA 2518909 p.Leu265Phe missense_variant 0.25
kasA 2518912 c.798G>T synonymous_variant 0.25
kasA 2519144 p.Gly344Cys missense_variant 0.17
kasA 2519343 p.Ala410Val missense_variant 0.2
eis 2714160 c.1173C>G synonymous_variant 0.29
eis 2714370 c.963C>A synonymous_variant 0.22
eis 2715195 c.138G>T synonymous_variant 0.18
eis 2715282 p.Phe17Leu missense_variant 0.17
eis 2715409 c.-77C>A upstream_gene_variant 0.29
ahpC 2726541 p.Glu117* stop_gained 0.4
ahpC 2726611 p.Pro140His missense_variant 0.4
ahpC 2726763 p.Leu191Ile missense_variant 0.33
folC 2746166 p.Ala478Asp missense_variant 0.33
folC 2746387 c.1212C>A synonymous_variant 0.25
folC 2746494 p.Glu369* stop_gained 0.27
folC 2746843 c.756C>A synonymous_variant 0.29
folC 2747185 c.414G>T synonymous_variant 0.18
folC 2747496 p.Asp35Tyr missense_variant 0.22
folC 2747679 c.-81C>A upstream_gene_variant 0.4
pepQ 2859535 p.Gly295Val missense_variant 0.29
pepQ 2859701 p.Gly240Cys missense_variant 0.25
pepQ 2860281 p.Phe46Leu missense_variant 0.25
ribD 2986818 c.-21C>T upstream_gene_variant 0.22
ribD 2986917 p.Glu27* stop_gained 0.33
ribD 2986925 c.87C>G synonymous_variant 0.29
ribD 2986985 p.Leu49Phe missense_variant 0.22
Rv2752c 3064661 p.Val511Leu missense_variant 0.25
Rv2752c 3065460 c.732G>T synonymous_variant 0.25
Rv2752c 3066029 p.Pro55Ser missense_variant 0.5
Rv2752c 3066125 p.Gly23Ser missense_variant 0.33
Rv2752c 3066319 c.-128T>G upstream_gene_variant 0.33
thyX 3067634 c.312C>A synonymous_variant 0.4
thyX 3067790 c.156C>A synonymous_variant 0.17
thyA 3073833 c.639C>A synonymous_variant 0.5
thyA 3073964 p.Leu170Met missense_variant 0.25
thyA 3073976 p.Arg166Ser missense_variant 0.25
thyA 3074153 p.Glu107* stop_gained 0.22
thyA 3074216 p.Asp86Tyr missense_variant 0.5
thyA 3074436 c.36C>A synonymous_variant 0.5
ald 3086649 c.-171C>A upstream_gene_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086825 c.6C>T synonymous_variant 0.33
ald 3087399 p.Val194Ile missense_variant 0.2
ald 3087725 c.906C>A synonymous_variant 0.19
Rv3083 3449411 p.Gly303Val missense_variant 0.15
Rv3083 3449442 c.939G>A synonymous_variant 0.18
Rv3083 3449621 p.Tyr373Cys missense_variant 0.2
fprA 3473984 c.-23G>T upstream_gene_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474276 c.270C>A synonymous_variant 0.5
fprA 3474753 c.747C>A synonymous_variant 0.18
fprA 3474934 p.Arg310Ser missense_variant 0.2
fprA 3475098 c.1092G>T synonymous_variant 0.22
whiB7 3568403 c.277T>C stop_lost&splice_region_variant 0.2
whiB7 3568533 p.Arg49Ser missense_variant 0.18
whiB7 3568675 p.Ser2* stop_gained 0.67
whiB7 3568758 c.-79C>A upstream_gene_variant 0.2
Rv3236c 3612069 p.Gly350Trp missense_variant 1.0
Rv3236c 3612103 p.Leu338Phe missense_variant 0.5
fbiB 3640593 c.-942C>A upstream_gene_variant 0.25
fbiA 3640621 p.Gln27Lys missense_variant 0.22
fbiB 3640755 c.-780C>A upstream_gene_variant 0.18
fbiA 3640766 p.Pro75His missense_variant 0.17
fbiA 3640876 p.His112Asn missense_variant 0.29
fbiA 3641378 p.Arg279Leu missense_variant 0.25
fbiB 3641543 c.9C>A synonymous_variant 0.29
fbiB 3642575 c.1041C>A synonymous_variant 0.31
alr 3840272 c.1149C>A synonymous_variant 0.18
alr 3840920 c.501G>T synonymous_variant 0.29
alr 3841006 p.Asp139Tyr missense_variant 0.22
alr 3841029 p.Ala131Val missense_variant 0.2
alr 3841293 p.Gly43Val missense_variant 0.25
alr 3841295 c.126G>T synonymous_variant 0.29
alr 3841375 p.Asp16Asn missense_variant 0.33
rpoA 3877890 c.618C>T synonymous_variant 0.67
rpoA 3878041 p.Gly156Val missense_variant 0.29
rpoA 3878060 p.Val150Met missense_variant 0.4
rpoA 3878359 p.Ala50Asp missense_variant 0.67
ddn 3986700 c.-144C>A upstream_gene_variant 0.15
ddn 3986738 c.-106C>A upstream_gene_variant 0.22
clpC1 4038408 p.Pro766Gln missense_variant 0.6
clpC1 4038767 c.1938G>T synonymous_variant 0.17
clpC1 4039244 c.1461G>T synonymous_variant 0.17
clpC1 4039678 p.Gln343* stop_gained 1.0
clpC1 4039954 p.Asp251Asn missense_variant 0.25
clpC1 4040669 c.36C>G synonymous_variant 0.5
clpC1 4040722 c.-18G>T upstream_gene_variant 0.29
embC 4239672 c.-191G>A upstream_gene_variant 0.22
embC 4239950 p.Arg30Trp missense_variant 0.18
embC 4240004 p.Pro48Thr missense_variant 0.22
embC 4240306 c.444C>A synonymous_variant 0.22
embC 4240850 p.Leu330Met missense_variant 0.15
embC 4241010 p.Gly383Asp missense_variant 0.17
embC 4241706 p.Ser615* stop_gained 0.5
embC 4242139 c.2277G>A synonymous_variant 0.25
embC 4242344 p.Ala828Thr missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242649 c.-584G>A upstream_gene_variant 0.18
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243865 c.633G>T synonymous_variant 0.15
embA 4243886 p.Met218Ile missense_variant 0.2
embA 4243966 p.Arg245Leu missense_variant 0.27
embA 4244159 c.927G>T synonymous_variant 0.33
embA 4244214 p.Ala328Thr missense_variant 0.2
embA 4244587 p.Leu452Pro missense_variant 0.13
embA 4244614 p.Ala461Val missense_variant 0.17
embA 4245404 c.2172C>A synonymous_variant 0.25
embB 4245791 c.-723C>A upstream_gene_variant 0.25
embA 4245822 p.Pro864Ser missense_variant 0.2
embB 4245905 c.-609C>A upstream_gene_variant 0.22
embB 4246232 c.-282C>A upstream_gene_variant 0.67
embB 4246660 c.147C>A synonymous_variant 0.18
embB 4246686 p.Trp58* stop_gained 0.18
embB 4247239 p.Leu242Phe missense_variant 0.29
embB 4247981 p.Leu490Met missense_variant 0.25
embB 4248392 p.Ala627Ser missense_variant 0.5
embB 4248536 p.Leu675Met missense_variant 0.17
aftB 4267384 p.Ala485Ser missense_variant 0.25
aftB 4267669 p.Ala390Thr missense_variant 0.29
aftB 4268150 p.Met229Ile missense_variant 0.5
aftB 4268187 p.Gly217Val missense_variant 1.0
aftB 4268731 p.Arg36Trp missense_variant 0.33
aftB 4268747 c.90C>T synonymous_variant 0.5
aftB 4268887 c.-51C>A upstream_gene_variant 0.2
ubiA 4269449 p.Val129Phe missense_variant 0.14
ubiA 4269491 p.Ala115Ser missense_variant 0.15
aftB 4269651 c.-815G>A upstream_gene_variant 0.25
ethA 4326011 p.Gly488Val missense_variant 0.25
ethA 4326065 p.Arg470His missense_variant 0.25
ethA 4326168 p.Pro436Thr missense_variant 0.33
ethA 4326190 p.Glu428Asp missense_variant 0.15
ethR 4326982 c.-567C>T upstream_gene_variant 0.25
ethA 4327028 p.Pro149Gln missense_variant 0.25
ethR 4327444 c.-105C>A upstream_gene_variant 0.33
ethA 4327458 p.Asp6Tyr missense_variant 0.29
ethA 4327608 c.-135C>T upstream_gene_variant 0.67
ethA 4327674 c.-201C>A upstream_gene_variant 0.25
ethR 4327777 p.Asp77Tyr missense_variant 0.25
ethR 4327807 c.260_261delTA frameshift_variant 0.25
ethA 4328112 c.-639G>T upstream_gene_variant 0.17
ethA 4328224 c.-751C>T upstream_gene_variant 0.25
whiB6 4338295 p.Trp76Leu missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338661 c.-140C>A upstream_gene_variant 0.17
whiB6 4338698 c.-177C>A upstream_gene_variant 0.15
gid 4407698 p.Asp169Tyr missense_variant 0.33
gid 4407731 c.472C>A synonymous_variant 0.33
gid 4407926 p.Pro93Thr missense_variant 0.25
gid 4408304 c.-102G>A upstream_gene_variant 0.15