TB-Profiler result

Run: ERR4821486
Summary

Run ID: ERR4821486

Sample name:

Date: 01-04-2023 17:16:45

Number of reads: 382118

Percentage reads mapped: 99.29

Strain: lineage2.2

Drug-resistance: Other

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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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 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
tlyA 1918211 p.Ala91Glu missense_variant 0.25 capreomycin
embB 4248488 p.Ala659Thr missense_variant 0.18 ethambutol
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 5114 c.-126C>A upstream_gene_variant 0.22
gyrB 5287 c.48T>C synonymous_variant 0.25
gyrB 5611 c.372C>A synonymous_variant 0.18
gyrB 5731 c.492C>T synonymous_variant 0.33
gyrB 6263 p.Asp342His missense_variant 0.22
gyrB 6664 p.Phe475Leu missense_variant 0.29
gyrB 6790 p.Phe517Leu missense_variant 0.14
gyrB 7087 p.Met616Ile missense_variant 0.14
gyrB 7097 p.Glu620* stop_gained 0.24
gyrB 7251 p.Arg671Gln missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7368 p.Glu23* stop_gained 0.15
gyrA 7406 c.105G>T synonymous_variant 0.13
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7642 p.Gly114Val missense_variant 0.17
gyrA 7986 p.Pro229Thr missense_variant 0.2
gyrA 8030 c.729C>A synonymous_variant 0.12
gyrA 8527 p.Arg409Leu missense_variant 0.2
gyrA 8632 p.Ala444Asp missense_variant 0.17
gyrA 8931 p.Val544Leu missense_variant 0.2
gyrA 8949 p.Lys550* stop_gained 0.13
gyrA 9036 p.Ala579Ser missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9801 p.Asp834Tyr missense_variant 0.29
fgd1 490748 c.-35G>T upstream_gene_variant 0.29
fgd1 491289 c.507C>A synonymous_variant 0.33
fgd1 491308 p.Ala176Thr missense_variant 0.5
fgd1 491603 p.Ala274Glu missense_variant 0.33
fgd1 491638 p.Val286Leu missense_variant 0.25
fgd1 491733 c.951G>A synonymous_variant 0.2
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575477 p.Pro44Thr missense_variant 0.15
mshA 575769 p.Ala141Glu missense_variant 0.13
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 575990 p.Val215Phe missense_variant 0.14
mshA 576082 p.Asp245Glu missense_variant 0.2
mshA 576505 c.1158C>T synonymous_variant 1.0
ccsA 619717 c.-174G>T upstream_gene_variant 0.4
ccsA 620251 p.Gly121Trp missense_variant 0.15
ccsA 620319 c.429C>A synonymous_variant 0.17
ccsA 620356 p.Leu156Val missense_variant 0.2
ccsA 620503 p.Glu205* stop_gained 0.25
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620629 p.Gly247Cys missense_variant 0.17
rpoB 760064 p.Glu86Asp missense_variant 0.17
rpoB 760426 p.Glu207Ala missense_variant 0.4
rpoB 761168 c.1362C>A synonymous_variant 0.25
rpoB 761258 p.Glu484Asp missense_variant 0.18
rpoB 761260 p.Gly485Val missense_variant 0.18
rpoB 761499 p.Val565Leu missense_variant 0.2
rpoB 761604 p.Leu600Ile missense_variant 0.25
rpoB 761881 p.Ala692Asp missense_variant 0.14
rpoB 761941 p.Asn712Ser missense_variant 0.15
rpoB 762148 p.Arg781Leu missense_variant 0.25
rpoB 762795 p.Asp997Tyr missense_variant 0.25
rpoB 762930 p.Pro1042Thr missense_variant 0.22
rpoB 762992 c.3190delG frameshift_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763223 c.-147C>A upstream_gene_variant 0.15
rpoC 763707 p.Arg113Leu missense_variant 0.14
rpoC 763804 p.His145Gln missense_variant 0.14
rpoC 763845 p.Arg159His missense_variant 0.2
rpoC 765052 c.1683C>G synonymous_variant 0.12
rpoC 765179 p.Gly604Trp missense_variant 0.15
rpoC 765400 c.2031G>T synonymous_variant 0.17
rpoC 765835 c.2466C>G synonymous_variant 0.33
rpoC 766211 p.Glu948* stop_gained 0.14
rpoC 766228 p.Leu953Phe missense_variant 0.12
rpoC 766696 p.Gln1109His missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776471 p.Gln670His missense_variant 0.14
mmpL5 776922 p.Ala520Asp missense_variant 0.15
mmpL5 777125 p.Ser452Arg missense_variant 0.17
mmpL5 777945 p.Pro179Arg missense_variant 0.14
mmpL5 778119 p.Thr121Asn missense_variant 0.12
mmpS5 778653 p.Ala85Ser missense_variant 0.18
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781383 c.-177G>T upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781700 c.141G>T synonymous_variant 0.17
fbiC 1302870 c.-61G>T upstream_gene_variant 0.17
fbiC 1303042 p.Thr38Ala missense_variant 0.29
fbiC 1303206 c.276C>T synonymous_variant 0.17
fbiC 1303328 p.Arg133Leu missense_variant 0.18
fbiC 1303417 p.Gly163Cys missense_variant 0.15
fbiC 1303546 p.Pro206Thr missense_variant 0.2
fbiC 1303932 c.1002G>T synonymous_variant 0.29
Rv1258c 1406456 c.885T>C synonymous_variant 0.2
Rv1258c 1406603 c.738G>A synonymous_variant 0.15
Rv1258c 1406621 c.720G>T synonymous_variant 0.17
Rv1258c 1406697 p.Gly215Ala missense_variant 0.2
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407264 p.Ser26* stop_gained 0.67
Rv1258c 1407282 p.Ala20Asp missense_variant 0.25
embR 1416502 p.Met282Ile missense_variant 0.2
embR 1416695 p.Ser218Tyr missense_variant 0.14
embR 1416988 c.360C>G synonymous_variant 0.5
embR 1417284 p.Thr22Ser missense_variant 0.12
atpE 1461233 c.189A>G synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471761 n.-85G>T upstream_gene_variant 0.19
rrs 1472063 n.218C>A non_coding_transcript_exon_variant 0.4
rrs 1472562 n.717C>A non_coding_transcript_exon_variant 0.18
rrs 1472577 n.732G>T non_coding_transcript_exon_variant 0.18
rrs 1472633 n.788C>A non_coding_transcript_exon_variant 0.29
rrs 1472768 n.923C>A non_coding_transcript_exon_variant 0.17
rrs 1473166 n.1321G>T non_coding_transcript_exon_variant 0.33
rrl 1473427 n.-231G>T upstream_gene_variant 0.2
rrl 1473548 n.-109delG upstream_gene_variant 0.14
rrl 1474372 n.715C>A non_coding_transcript_exon_variant 0.33
rrl 1474661 n.1004G>T non_coding_transcript_exon_variant 0.17
rrl 1474857 n.1200G>T non_coding_transcript_exon_variant 0.29
rrl 1475520 n.1863G>T non_coding_transcript_exon_variant 0.33
rrl 1475993 n.2336C>A non_coding_transcript_exon_variant 0.17
rrl 1476744 n.3087G>T non_coding_transcript_exon_variant 0.18
fabG1 1673195 c.-245C>G upstream_gene_variant 0.22
fabG1 1673329 c.-111A>G upstream_gene_variant 0.11
fabG1 1673699 p.Ser87Tyr missense_variant 0.2
fabG1 1674118 p.Glu227* stop_gained 0.5
inhA 1674295 p.Gln32Lys missense_variant 0.22
rpsA 1833426 c.-116T>A upstream_gene_variant 0.5
rpsA 1833599 p.Glu20* stop_gained 0.15
rpsA 1833628 c.87G>A synonymous_variant 0.15
rpsA 1833745 c.204G>T synonymous_variant 0.13
rpsA 1833903 p.Glu121Gly missense_variant 0.67
rpsA 1833933 p.Ile131Thr missense_variant 0.29
rpsA 1833972 p.Leu144Pro missense_variant 0.2
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834239 p.Gly233Val missense_variant 0.18
rpsA 1834324 p.Glu261Asp missense_variant 0.17
rpsA 1834328 p.Leu263Ile missense_variant 0.17
rpsA 1834353 p.Arg271Leu missense_variant 0.17
rpsA 1834373 p.Ala278Ser missense_variant 0.17
rpsA 1834429 c.888C>T synonymous_variant 0.29
rpsA 1834484 p.Glu315* stop_gained 0.5
rpsA 1834754 p.Glu405* stop_gained 0.15
tlyA 1917858 c.-82G>T upstream_gene_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918365 p.Glu142Asp missense_variant 0.33
tlyA 1918741 p.Pro268Ala missense_variant 0.2
ndh 2101878 p.Gly389Arg missense_variant 0.12
ndh 2102079 p.Asp322Asn missense_variant 0.22
katG 2154206 p.Ala636Thr missense_variant 0.17
katG 2154207 c.1905C>A synonymous_variant 0.17
katG 2154329 p.Arg595* stop_gained 0.33
katG 2154608 p.Gln502Lys missense_variant 0.15
katG 2154617 p.Leu499Met missense_variant 0.18
katG 2154636 c.1476C>G synonymous_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154775 p.Ser446Ile missense_variant 1.0
katG 2155958 p.Pro52Thr missense_variant 0.18
katG 2156065 p.Ala16Asp missense_variant 0.13
katG 2156097 p.His5Gln missense_variant 0.12
katG 2156153 c.-42C>T upstream_gene_variant 0.13
katG 2156211 c.-100G>T upstream_gene_variant 0.12
katG 2156245 c.-134G>A upstream_gene_variant 0.18
PPE35 2167692 p.Gly974Asp missense_variant 0.14
PPE35 2167877 p.Ser912Arg missense_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168041 p.Ala858Thr missense_variant 0.33
PPE35 2168270 c.2343G>T synonymous_variant 0.12
PPE35 2169023 c.1590G>T synonymous_variant 0.17
PPE35 2169542 c.1071C>A synonymous_variant 0.13
PPE35 2169651 p.Leu321Ser missense_variant 0.13
PPE35 2169794 c.819C>A synonymous_variant 0.18
Rv1979c 2221809 c.1356C>T synonymous_variant 0.2
Rv1979c 2221843 p.Arg441Leu missense_variant 0.25
Rv1979c 2221881 c.1284G>A synonymous_variant 0.17
Rv1979c 2222189 p.Leu326Ile missense_variant 0.13
Rv1979c 2222286 c.879G>T synonymous_variant 0.25
Rv1979c 2222404 p.Arg254Ile missense_variant 0.13
Rv1979c 2222441 p.Ala242Ser missense_variant 0.17
Rv1979c 2222603 p.Gln188Lys missense_variant 0.17
Rv1979c 2222789 p.Ala126Ser missense_variant 0.13
Rv1979c 2222847 p.Trp106Cys missense_variant 0.13
Rv1979c 2222991 c.174G>T synonymous_variant 0.25
Rv1979c 2223110 p.Val19Ile missense_variant 0.15
Rv1979c 2223266 c.-102G>C upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223324 c.-160G>T upstream_gene_variant 0.18
pncA 2289621 c.-380C>A upstream_gene_variant 0.22
pncA 2290233 c.-992C>A upstream_gene_variant 0.29
kasA 2518094 c.-21G>T upstream_gene_variant 0.17
kasA 2518347 p.Arg78Gln missense_variant 0.29
kasA 2518621 c.507G>T synonymous_variant 0.18
kasA 2518769 p.Arg219Ser missense_variant 0.67
eis 2714139 c.1194C>A synonymous_variant 0.18
eis 2714663 p.Ala224Ser missense_variant 0.29
eis 2714710 p.Pro208His missense_variant 0.4
eis 2714814 c.519C>A synonymous_variant 0.5
eis 2714834 p.Arg167Gly missense_variant 0.5
eis 2715324 c.9G>T synonymous_variant 0.18
ahpC 2725921 c.-272A>T upstream_gene_variant 1.0
ahpC 2726054 c.-139C>A upstream_gene_variant 0.15
ahpC 2726294 c.102C>T synonymous_variant 0.15
folC 2746807 c.792G>A synonymous_variant 0.13
folC 2746831 c.768G>T synonymous_variant 0.13
folC 2746896 p.Gly235Trp missense_variant 0.29
folC 2746948 c.651G>T synonymous_variant 0.25
folC 2747142 p.Glu153* stop_gained 0.22
pepQ 2859350 p.Gln357Lys missense_variant 0.25
pepQ 2859355 p.Ala355Asp missense_variant 0.18
pepQ 2859753 p.Phe222Leu missense_variant 0.25
pepQ 2859910 p.Arg170Leu missense_variant 0.33
pepQ 2860254 c.165C>A synonymous_variant 0.29
ribD 2986783 c.-56C>A upstream_gene_variant 0.2
ribD 2987096 c.258C>A synonymous_variant 0.29
ribD 2987256 p.Pro140Thr missense_variant 0.33
ribD 2987541 p.Leu235Met missense_variant 0.4
Rv2752c 3064778 p.Phe472Leu missense_variant 0.2
Rv2752c 3065163 c.1029C>A synonymous_variant 0.2
Rv2752c 3065361 c.831C>A synonymous_variant 0.17
Rv2752c 3065705 p.Gly163* stop_gained 0.22
Rv2752c 3066134 p.Ala20Thr missense_variant 0.14
Rv2752c 3066357 c.-166G>A upstream_gene_variant 0.22
thyX 3067413 p.Ala178Asp missense_variant 0.29
thyX 3067505 c.441G>T synonymous_variant 0.18
thyA 3073803 p.Glu223Asp missense_variant 0.29
thyA 3074234 p.Trp80Arg missense_variant 0.18
thyA 3074555 c.-84C>A upstream_gene_variant 0.15
thyA 3074566 c.-95G>T upstream_gene_variant 0.15
ald 3086684 c.-136G>T upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086981 c.162C>A synonymous_variant 0.25
ald 3087020 p.Asp67Glu missense_variant 0.18
ald 3087198 p.Leu127Ile missense_variant 0.14
ald 3087794 c.975C>T synonymous_variant 0.25
ald 3087821 c.1002G>T synonymous_variant 0.2
fbiD 3339087 c.-31C>A upstream_gene_variant 0.18
fbiD 3339306 c.189C>A synonymous_variant 0.4
fbiD 3339372 c.255C>A synonymous_variant 0.5
fbiD 3339728 p.Gly204Val missense_variant 0.15
Rv3083 3448389 c.-115C>A upstream_gene_variant 0.29
Rv3083 3449010 p.Trp169* stop_gained 0.14
Rv3083 3449147 p.Ser215* stop_gained 0.5
Rv3083 3449193 c.690G>T synonymous_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474453 c.447G>A synonymous_variant 0.13
fprA 3474455 p.Ala150Asp missense_variant 0.13
fprA 3475311 p.Glu435Asp missense_variant 0.33
whiB7 3568576 p.Gly35Val missense_variant 0.18
Rv3236c 3612060 p.Ala353Thr missense_variant 0.14
Rv3236c 3612518 p.Tyr200Cys missense_variant 0.4
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612838 c.279G>T synonymous_variant 0.33
Rv3236c 3612978 p.Gly47Ser missense_variant 0.25
Rv3236c 3613001 p.Ala39Gly missense_variant 0.14
Rv3236c 3613165 c.-49G>T upstream_gene_variant 0.14
fbiA 3640618 p.Gly26Ser missense_variant 0.22
fbiA 3640627 p.Ala29Ser missense_variant 0.22
fbiA 3640907 p.Gly122Val missense_variant 0.22
fbiB 3642036 p.Ala168Ser missense_variant 0.33
fbiB 3642309 p.Leu259Met missense_variant 0.25
fbiB 3642350 c.816G>T synonymous_variant 0.22
fbiB 3642380 p.Glu282Asp missense_variant 0.17
fbiB 3642847 p.Pro438Gln missense_variant 0.5
alr 3840459 p.Ser321* stop_gained 0.2
alr 3840671 c.750G>A synonymous_variant 0.22
alr 3840894 p.Leu176Gln missense_variant 0.25
alr 3841014 p.Arg136Pro missense_variant 0.22
alr 3841030 p.Ala131Ser missense_variant 0.18
alr 3841507 c.-87C>T upstream_gene_variant 0.13
alr 3841515 c.-95C>A upstream_gene_variant 0.13
rpoA 3877722 p.Asn262Lys missense_variant 0.33
rpoA 3877760 p.Pro250Thr missense_variant 0.2
rpoA 3877811 p.Glu233* stop_gained 0.22
rpoA 3877899 p.Ser203Arg missense_variant 0.17
rpoA 3878319 p.Phe63Leu missense_variant 0.15
rpoA 3878503 p.Leu2Gln missense_variant 0.4
ddn 3986742 c.-102G>A upstream_gene_variant 0.25
ddn 3986749 c.-95C>A upstream_gene_variant 0.22
clpC1 4038398 c.2307G>T synonymous_variant 0.14
clpC1 4038750 p.Gly652Val missense_variant 0.5
clpC1 4039208 c.1497C>A synonymous_variant 0.29
clpC1 4039325 p.Gln460His missense_variant 0.15
clpC1 4039793 c.912C>G synonymous_variant 0.12
clpC1 4040314 p.Leu131Met missense_variant 0.29
clpC1 4040375 c.330G>T synonymous_variant 0.17
clpC1 4040894 c.-190G>T upstream_gene_variant 0.25
panD 4043967 c.315C>A synonymous_variant 0.4
embC 4240585 c.723C>A synonymous_variant 0.29
embC 4241026 c.1164C>G synonymous_variant 0.29
embC 4241507 p.Ala549Thr missense_variant 0.13
embC 4241706 p.Ser615Leu missense_variant 0.22
embC 4242090 p.Ala743Val missense_variant 0.29
embC 4242629 p.Ala923Ser missense_variant 0.22
embC 4242641 p.Arg927Ser missense_variant 0.22
embC 4242771 p.Thr970Lys missense_variant 0.4
embA 4242856 c.-377C>A upstream_gene_variant 0.33
embA 4243315 p.Cys28Phe missense_variant 0.2
embA 4243318 p.Gly29Val missense_variant 0.2
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244813 p.Cys527* stop_gained 0.14
embA 4244877 p.Ala549Ser missense_variant 0.29
embA 4244904 p.Val558Leu missense_variant 1.0
embA 4244918 c.1686G>T synonymous_variant 0.17
embA 4245404 c.2172C>G synonymous_variant 0.18
embB 4245545 c.-969C>T upstream_gene_variant 0.29
embA 4245569 p.Glu779Asp missense_variant 0.22
embA 4245682 p.Gly817Val missense_variant 0.29
embB 4246331 c.-183C>G upstream_gene_variant 0.4
embB 4247344 c.831C>T synonymous_variant 0.18
embB 4247425 c.912G>A synonymous_variant 0.17
embB 4247435 p.Arg308* stop_gained 0.25
embB 4247779 c.1266C>A synonymous_variant 0.22
embB 4247969 p.Gly486Arg missense_variant 0.67
embB 4248171 p.Ala553Glu missense_variant 0.25
embB 4248204 p.Pro564Arg missense_variant 0.25
embB 4248280 c.1767C>A synonymous_variant 0.12
embB 4248292 c.1779G>T synonymous_variant 0.14
embB 4248840 p.Pro776His missense_variant 0.17
embB 4248915 p.Ala801Glu missense_variant 0.33
embB 4249687 c.3174C>A synonymous_variant 0.17
embB 4249754 p.Gly1081Cys missense_variant 0.17
aftB 4267329 p.Arg503Leu missense_variant 0.4
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267814 c.1023G>T synonymous_variant 0.22
aftB 4267827 p.Arg337Pro missense_variant 0.29
aftB 4268033 c.804G>T synonymous_variant 0.12
aftB 4268186 c.651C>A synonymous_variant 0.22
aftB 4268402 p.Leu145Phe missense_variant 0.15
ubiA 4269417 p.Cys139* stop_gained 0.25
aftB 4269492 c.-656G>T upstream_gene_variant 0.25
ubiA 4269866 c.-33G>C upstream_gene_variant 0.33
ubiA 4269891 c.-58G>T upstream_gene_variant 0.33
ethA 4326020 p.Ala485Asp missense_variant 0.2
ethA 4326305 p.Ser390Tyr missense_variant 0.2
ethA 4326380 p.Thr365Lys missense_variant 0.33
ethA 4326735 p.Ala247Ser missense_variant 0.13
ethR 4326997 c.-552C>A upstream_gene_variant 0.33
ethR 4327084 c.-465G>A upstream_gene_variant 1.0
ethA 4327216 p.Lys86Asn missense_variant 0.25
ethA 4327262 p.Gly71Ala missense_variant 0.33
ethA 4327421 p.Ser18Ile missense_variant 0.14
ethR 4328193 p.Asn215Lys missense_variant 0.33
ethA 4328212 c.-739G>T upstream_gene_variant 0.29
ethA 4328262 c.-789C>A upstream_gene_variant 0.18
whiB6 4338182 p.Gln114Lys missense_variant 0.18
whiB6 4338277 p.Pro82His missense_variant 0.33
whiB6 4338284 p.Val80Ile missense_variant 0.33
whiB6 4338437 p.Val29Phe missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338712 c.-191T>C upstream_gene_variant 0.12
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4407975 c.228C>A synonymous_variant 0.15
gid 4408143 c.60G>T synonymous_variant 0.14