TB-Profiler result

Run: SRR7535077
Summary

Run ID: SRR7535077

Sample name:

Date: 04-04-2023 19:44:04

Number of reads: 1036028

Percentage reads mapped: 10.4

Strain: lineage4.6.1.2

Drug-resistance: MDR-TB

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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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.1 Euro-American (Uganda) T2 RD724 0.99
lineage4.6.1.2 Euro-American T2 RD724 0.98
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
rpoB 760663 p.Ala286Val missense_variant 0.2 rifampicin
rpoB 761099 p.Ser431Arg missense_variant 0.12 rifampicin
katG 2155692 p.Ser140Asn missense_variant 0.22 isoniazid
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 5188 c.-52C>G upstream_gene_variant 0.14
gyrB 6291 p.Arg351Leu missense_variant 0.17
gyrA 6589 c.-713G>T upstream_gene_variant 0.25
gyrA 6628 c.-674C>A upstream_gene_variant 0.14
gyrB 6861 p.Ser541Tyr missense_variant 0.14
gyrB 6890 p.Phe551Ile missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7539 p.Thr80Ala missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7729 p.Arg143Met missense_variant 0.33
gyrA 7974 p.Gly225Ser missense_variant 0.11
gyrA 9258 p.Leu653Val missense_variant 0.12
gyrA 9292 p.Leu664Pro missense_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9404 p.Gln701His missense_variant 0.11
fgd1 491198 p.Met139Lys missense_variant 0.17
fgd1 491556 p.Gln258His missense_variant 0.17
fgd1 491609 p.Pro276Gln missense_variant 0.17
mshA 576466 c.1119G>A synonymous_variant 0.17
mshA 576475 c.1128G>A synonymous_variant 0.2
rpoB 759955 c.151delC frameshift_variant 0.17
rpoB 760254 p.Asp150Tyr missense_variant 0.11
rpoB 760298 c.492G>T synonymous_variant 0.11
rpoB 760695 p.Glu297* stop_gained 0.25
rpoB 760944 p.Gln380Lys missense_variant 0.33
rpoB 761191 p.Ala462Val missense_variant 0.11
rpoB 761214 p.His470Tyr missense_variant 0.17
rpoC 762833 c.-537C>T upstream_gene_variant 0.17
rpoC 762894 c.-476C>T upstream_gene_variant 0.17
rpoB 762911 p.Ile1035Met missense_variant 0.33
rpoC 762923 c.-447C>G upstream_gene_variant 0.3
rpoC 762929 c.-441G>T upstream_gene_variant 0.27
rpoC 762932 c.-438G>T upstream_gene_variant 0.27
rpoB 762939 p.Met1045Leu missense_variant 0.27
rpoB 762942 p.Ile1046Val missense_variant 0.25
rpoC 762947 c.-423C>G upstream_gene_variant 0.23
rpoC 762962 c.-408C>T upstream_gene_variant 0.23
rpoC 762989 c.-381G>T upstream_gene_variant 0.18
rpoC 762998 c.-372G>A upstream_gene_variant 0.2
rpoC 763004 c.-366G>A upstream_gene_variant 0.11
rpoC 763654 p.Ile95Met missense_variant 0.25
rpoC 763714 c.345G>C synonymous_variant 0.12
rpoC 763717 c.348T>C synonymous_variant 0.12
rpoC 763723 c.354G>C synonymous_variant 0.12
rpoC 763729 c.360G>C synonymous_variant 0.12
rpoC 763744 c.375G>C synonymous_variant 0.11
rpoC 763792 p.Glu141Asp missense_variant 0.12
rpoC 763801 c.432C>G synonymous_variant 0.12
rpoC 763807 c.438T>C synonymous_variant 0.17
rpoC 764310 p.Leu314His missense_variant 0.2
rpoC 765309 p.Glu647Gly missense_variant 0.12
rpoC 766936 c.3567G>A synonymous_variant 0.25
rpoC 767033 p.Ser1222Thr missense_variant 0.2
mmpL5 775591 p.Val964Phe missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775927 c.2554C>T synonymous_variant 0.33
mmpL5 775931 c.2550C>T synonymous_variant 0.5
mmpL5 775965 p.Ala839Gly missense_variant 0.2
mmpL5 776634 p.Asp616Ala missense_variant 0.12
mmpL5 776676 p.Ser602Leu missense_variant 0.14
mmpL5 777131 c.1350C>A synonymous_variant 0.17
mmpL5 777259 p.Leu408Met missense_variant 0.2
mmpL5 777260 c.1221C>A synonymous_variant 0.2
mmpL5 777296 c.1185C>A synonymous_variant 0.12
mmpL5 777452 p.Met343Ile missense_variant 0.2
mmpL5 777478 p.Leu335Ile missense_variant 0.17
mmpL5 778409 c.71delT frameshift_variant 0.12
rpsL 781365 c.-195_-194insTG upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800644 c.-165G>A upstream_gene_variant 0.11
rplC 801115 p.Ala103Pro missense_variant 0.12
fbiC 1304427 c.1497G>T synonymous_variant 0.11
fbiC 1304443 c.1514delC frameshift_variant 0.12
Rv1258c 1406481 c.859dupC frameshift_variant 0.1
Rv1258c 1406522 c.819G>T synonymous_variant 0.12
Rv1258c 1406807 c.534G>A synonymous_variant 0.11
Rv1258c 1407058 p.Gly95Trp missense_variant 0.11
embR 1416410 p.Leu313Arg missense_variant 1.0
embR 1416821 p.Ala176Asp missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472120 n.275G>C non_coding_transcript_exon_variant 0.5
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.5
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.5
rrs 1472129 n.284G>T non_coding_transcript_exon_variant 0.5
rrs 1472135 n.290C>T non_coding_transcript_exon_variant 0.33
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.33
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.33
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.33
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.33
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.6
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.86
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.95
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.95
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.95
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.9
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.9
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.89
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.89
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.93
rrs 1472278 n.433C>T non_coding_transcript_exon_variant 0.5
rrs 1472279 n.434T>G non_coding_transcript_exon_variant 0.5
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 0.25
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.67
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.5
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.5
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.5
rrs 1472544 n.699C>G non_coding_transcript_exon_variant 0.5
rrs 1472545 n.700A>C non_coding_transcript_exon_variant 0.5
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 1.0
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 1.0
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.86
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.83
rrs 1472785 n.940G>T non_coding_transcript_exon_variant 0.71
rrs 1472786 n.941C>G non_coding_transcript_exon_variant 0.71
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.83
rrs 1472814 n.969G>A non_coding_transcript_exon_variant 0.8
rrs 1472824 n.979T>C non_coding_transcript_exon_variant 0.5
rrs 1473139 n.1294T>C non_coding_transcript_exon_variant 0.5
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.5
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.5
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.75
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.75
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.75
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.75
rrs 1473198 n.1354delC non_coding_transcript_exon_variant 0.75
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.75
rrs 1473204 n.1359C>T non_coding_transcript_exon_variant 0.75
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.75
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.86
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 1.0
rrl 1474146 n.489G>T non_coding_transcript_exon_variant 1.0
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 1.0
rrl 1474569 n.912A>G non_coding_transcript_exon_variant 1.0
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.25
rrl 1475787 n.2130C>T non_coding_transcript_exon_variant 0.25
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.33
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.33
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.67
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.75
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.91
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.91
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.93
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.93
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.93
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.94
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 1.0
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 1.0
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 1.0
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 1.0
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 1.0
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 1.0
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 1.0
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 1.0
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 1.0
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 1.0
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 1.0
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.8
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.8
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.75
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.75
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.75
rrl 1476483 n.2826G>A non_coding_transcript_exon_variant 0.6
fabG1 1673242 c.-198C>G upstream_gene_variant 0.11
fabG1 1673627 p.Thr63Ser missense_variant 0.2
inhA 1674465 c.264C>T synonymous_variant 1.0
inhA 1674625 p.Gly142Ser missense_variant 0.25
rpsA 1833686 p.Asp49His missense_variant 0.25
rpsA 1833938 p.Val133Leu missense_variant 0.2
rpsA 1834823 p.His428Asn missense_variant 0.12
rpsA 1834847 p.Ala436Thr missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153970 p.Asp714Glu missense_variant 0.33
katG 2154677 p.Ala479Ser missense_variant 0.25
katG 2154758 p.Glu452Lys missense_variant 0.5
katG 2154772 p.His447Leu missense_variant 0.5
katG 2154873 p.Tyr413* stop_gained 0.33
katG 2154879 c.1233C>T synonymous_variant 0.33
katG 2155377 c.735G>T synonymous_variant 0.25
katG 2155650 c.462G>A synonymous_variant 0.11
katG 2155655 p.Lys153Gln missense_variant 0.2
katG 2155668 c.444G>C synonymous_variant 0.2
katG 2155674 c.438G>C synonymous_variant 0.25
katG 2155691 c.421T>C synonymous_variant 0.22
katG 2155716 c.396T>C synonymous_variant 0.33
katG 2155719 c.393G>A synonymous_variant 0.17
katG 2156439 c.-328T>C upstream_gene_variant 0.17
PPE35 2168328 p.Pro762Leu missense_variant 0.33
PPE35 2168820 p.Ala598Gly missense_variant 0.25
PPE35 2168999 c.1614G>C synonymous_variant 0.33
PPE35 2169387 p.Thr409Ile missense_variant 0.2
PPE35 2169397 p.Gly406Ser missense_variant 0.2
PPE35 2169496 p.Asp373Tyr missense_variant 0.33
Rv1979c 2221824 p.Phe447Leu missense_variant 0.2
Rv1979c 2221879 p.Ala429Glu missense_variant 0.17
Rv1979c 2222059 p.Phe369Cys missense_variant 0.5
Rv1979c 2222069 p.Ala366Thr missense_variant 0.5
Rv1979c 2222616 p.Trp183Cys missense_variant 0.17
Rv1979c 2222641 p.Ser175* stop_gained 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289502 c.-261G>T upstream_gene_variant 0.11
pncA 2289575 c.-334G>T upstream_gene_variant 0.12
pncA 2290217 c.-976T>G upstream_gene_variant 0.17
kasA 2518093 c.-22C>A upstream_gene_variant 0.2
kasA 2518457 p.Gly115Arg missense_variant 0.17
kasA 2518582 c.468G>A synonymous_variant 0.12
eis 2715016 p.Arg106Pro missense_variant 0.11
ahpC 2726031 c.-162C>A upstream_gene_variant 0.25
ahpC 2726323 p.Pro44Gln missense_variant 0.17
ahpC 2726421 p.Asp77Tyr missense_variant 0.14
ahpC 2726536 p.Lys115Met missense_variant 0.2
folC 2746434 p.Gly389Ser missense_variant 0.12
folC 2746676 p.Ser308Tyr missense_variant 0.12
ribD 2987327 c.489C>A synonymous_variant 0.12
Rv2752c 3065414 p.Ser260Ala missense_variant 0.17
Rv2752c 3065472 c.720C>A synonymous_variant 0.14
Rv2752c 3065558 p.Gly212Trp missense_variant 0.25
thyA 3073806 c.666C>G synonymous_variant 0.17
thyA 3074355 c.117G>T synonymous_variant 0.14
ald 3086767 c.-53A>T upstream_gene_variant 1.0
ald 3086901 p.Arg28Ser missense_variant 0.14
ald 3086913 p.Glu32* stop_gained 0.17
ald 3086938 p.Gly40Val missense_variant 0.33
ald 3087585 p.Ala256Thr missense_variant 0.14
fbiD 3339399 c.282C>A synonymous_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474097 p.Asp31Tyr missense_variant 0.12
fprA 3474605 p.Arg200Leu missense_variant 0.11
fprA 3475262 p.Thr419Arg missense_variant 0.14
Rv3236c 3612944 p.Ile58Ser missense_variant 0.1
Rv3236c 3613020 p.Ile33Leu missense_variant 0.12
Rv3236c 3613081 c.36C>A synonymous_variant 0.17
Rv3236c 3613159 c.-43G>T upstream_gene_variant 0.14
Rv3236c 3613230 c.-118_-115delGATG upstream_gene_variant 0.14
fbiA 3641344 p.Thr268Ala missense_variant 0.14
fbiB 3642772 p.Asp413Ala missense_variant 0.25
rpoA 3877664 p.Asp282Asn missense_variant 0.14
clpC1 4038607 p.Glu700Lys missense_variant 0.14
clpC1 4038641 p.Asn688Lys missense_variant 0.11
clpC1 4039239 p.Gly489Asp missense_variant 0.17
clpC1 4040241 p.Thr155Phe missense_variant 0.14
clpC1 4040249 p.Glu152Gly missense_variant 0.12
embC 4241771 p.Val637Phe missense_variant 0.25
embC 4241794 c.1932C>A synonymous_variant 0.12
embC 4242450 p.Met863Arg missense_variant 0.12
embC 4242545 p.Glu895Lys missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244703 p.Pro491Ser missense_variant 0.17
embA 4244712 p.Ala494Ser missense_variant 0.17
embA 4245055 p.Thr608Asn missense_variant 1.0
embA 4245148 p.Pro639Leu missense_variant 0.2
embB 4246635 p.Ser41Leu missense_variant 0.14
embB 4248584 p.Arg691Ser missense_variant 0.11
embB 4249533 p.Ala1007Asp missense_variant 0.17
embB 4249542 p.Pro1010Gln missense_variant 0.2
embB 4249697 p.Gly1062Ser missense_variant 0.33
embB 4249745 p.Leu1078Ile missense_variant 0.2
aftB 4267404 p.Pro478Arg missense_variant 0.17
aftB 4268565 p.Ser91Trp missense_variant 0.2
ubiA 4269287 p.Gly183Ser missense_variant 0.14
ubiA 4269859 c.-26A>G upstream_gene_variant 0.11
ethR 4326820 c.-729C>A upstream_gene_variant 0.25
ethA 4327686 c.-213C>T upstream_gene_variant 0.2
ethR 4327693 p.Asp49Asn missense_variant 0.17
ethR 4328038 p.Arg164Cys missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338635 c.-114A>C upstream_gene_variant 1.0