TB-Profiler result

Run: SRR21277805
Summary

Run ID: SRR21277805

Sample name:

Date: 04-04-2023 01:44:09

Number of reads: 14188688

Percentage reads mapped: 98.24

Strain: lineage2.2.1.1

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
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 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
gyrA 7572 p.Ser91Pro missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
embB 4247850 p.Pro446His missense_variant 0.5 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7460 c.159C>A synonymous_variant 0.14
gyrA 7541 c.240C>A synonymous_variant 0.1
gyrA 7549 p.Asn83Ile missense_variant 0.1
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7619 c.318C>A synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9312 p.Leu671Met missense_variant 0.12
fgd1 490682 c.-101C>A upstream_gene_variant 0.33
fgd1 490694 c.-89G>T upstream_gene_variant 0.16
fgd1 491311 p.Gly177Ser missense_variant 0.19
fgd1 491347 p.Gly189Cys missense_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575287 c.-61A>T upstream_gene_variant 0.12
mshA 575534 p.Gly63Cys missense_variant 0.11
mshA 575655 p.Val103Glu missense_variant 0.1
mshA 575661 p.Pro105His missense_variant 0.12
mshA 575663 p.Gly106Arg missense_variant 0.11
mshA 575892 p.Ala182Val missense_variant 0.22
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 575919 p.Gly191Val missense_variant 0.14
mshA 576254 p.Gly303Cys missense_variant 0.23
mshA 576450 p.Pro368Gln missense_variant 0.4
mshA 576709 c.1362C>A synonymous_variant 0.5
mshA 576742 c.1395G>T synonymous_variant 0.33
mshA 576751 p.Lys468Asn missense_variant 0.14
ccsA 619818 c.-73G>T upstream_gene_variant 0.14
ccsA 619924 p.Arg12Ser missense_variant 0.16
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760453 p.Val216Asp missense_variant 0.12
rpoB 760457 c.651C>T synonymous_variant 0.14
rpoB 761210 c.1404C>T synonymous_variant 0.14
rpoB 761458 p.Pro551Gln missense_variant 0.11
rpoB 761658 p.Pro618Lys missense_variant 0.12
rpoB 761691 p.Ala629Ser missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763969 c.600C>T synonymous_variant 0.15
rpoC 763971 p.Gly201Val missense_variant 0.11
rpoC 764547 p.Gly393Glu missense_variant 0.15
rpoC 764551 c.1182G>A synonymous_variant 0.15
rpoC 764560 c.1191T>A synonymous_variant 0.4
rpoC 765278 p.Leu637Met missense_variant 0.11
rpoC 765282 p.Thr638Asn missense_variant 0.15
rpoC 766136 p.Arg923Trp missense_variant 0.13
rpoC 766482 p.Arg1038Gln missense_variant 0.12
rpoC 766967 p.Pro1200Thr missense_variant 0.17
rpoC 766993 p.Met1208Ile missense_variant 0.11
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 777283 c.1198C>T synonymous_variant 0.1
mmpL5 777393 p.Arg363Gln missense_variant 0.1
mmpL5 779352 c.-872C>T upstream_gene_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801234 c.426G>A synonymous_variant 0.2
fbiC 1303093 p.Leu55Ile missense_variant 0.13
fbiC 1303098 c.168C>A synonymous_variant 0.27
fbiC 1303134 c.204G>T synonymous_variant 0.15
fbiC 1303135 p.Gly69Cys missense_variant 0.11
fbiC 1304432 p.Ser501* stop_gained 0.12
fbiC 1304478 c.1548G>T synonymous_variant 0.11
fbiC 1305459 c.2529G>A synonymous_variant 1.0
Rv1258c 1406170 p.Gly391Arg missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 0.98
Rv1258c 1406988 p.Pro118Leu missense_variant 0.25
Rv1258c 1407515 c.-175G>T upstream_gene_variant 0.12
Rv1258c 1407517 c.-177G>T upstream_gene_variant 0.18
Rv1258c 1407519 c.-179C>T upstream_gene_variant 0.33
embR 1416473 p.Leu292Gln missense_variant 0.18
embR 1416962 p.Gly129Phe missense_variant 0.1
embR 1416974 p.Ala125Glu missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674430 p.Arg77Trp missense_variant 0.13
inhA 1674822 c.621C>A synonymous_variant 0.13
inhA 1674857 p.Glu219Val missense_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834862 p.Ala441Thr missense_variant 0.12
rpsA 1834920 p.Ala460Val missense_variant 0.11
tlyA 1917955 p.Arg6Ser missense_variant 0.24
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918072 p.Ala45Ser missense_variant 0.4
tlyA 1918323 c.384G>T synonymous_variant 0.21
tlyA 1918333 p.Glu132* stop_gained 0.17
tlyA 1918555 c.616C>A synonymous_variant 0.11
tlyA 1918584 c.645A>T synonymous_variant 0.38
tlyA 1918610 p.Gly224Val missense_variant 0.1
ndh 2101684 p.Gln453Tyr missense_variant 0.14
ndh 2101699 c.1344G>A synonymous_variant 0.12
ndh 2102200 c.843G>T synonymous_variant 0.18
ndh 2102208 p.Gly279Trp missense_variant 0.14
ndh 2102230 c.813G>A synonymous_variant 0.11
ndh 2102374 c.669G>A synonymous_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155737 p.Gly125Val missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170025 c.588G>T synonymous_variant 0.12
PPE35 2170032 p.Gly194Val missense_variant 0.4
PPE35 2170349 c.264C>T synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518593 p.Ala160Asp missense_variant 0.15
kasA 2518725 p.Ala204Val missense_variant 0.13
kasA 2518871 p.His253Tyr missense_variant 1.0
kasA 2519179 c.1065G>T synonymous_variant 0.22
eis 2714846 p.Val163Ile missense_variant 1.0
eis 2714903 c.430C>A synonymous_variant 0.25
eis 2715025 p.Glu103Val missense_variant 0.33
eis 2715057 p.Arg92Gln missense_variant 0.33
eis 2715562 c.-230G>T upstream_gene_variant 0.15
eis 2715565 c.-233C>T upstream_gene_variant 0.22
folC 2746255 c.1344C>T synonymous_variant 0.1
folC 2746374 p.Pro409Thr missense_variant 0.2
folC 2746376 p.Ser408* stop_gained 0.11
folC 2746570 c.1029C>T synonymous_variant 0.11
folC 2746635 p.Asp322Asn missense_variant 0.14
folC 2746636 c.963C>A synonymous_variant 0.11
folC 2746827 p.Arg258Trp missense_variant 0.1
folC 2747119 p.Phe160Leu missense_variant 0.12
folC 2747344 c.255G>A synonymous_variant 0.14
folC 2747348 p.Ala84Glu missense_variant 0.14
folC 2747772 c.-174C>T upstream_gene_variant 0.29
pepQ 2859588 c.831G>T synonymous_variant 0.1
pepQ 2859596 p.Ala275Ser missense_variant 0.14
pepQ 2859623 p.Pro266Thr missense_variant 0.17
pepQ 2859954 c.465C>A synonymous_variant 0.38
pepQ 2859959 p.Leu154Met missense_variant 0.15
pepQ 2859965 p.Ala152Thr missense_variant 0.17
pepQ 2860583 c.-165G>T upstream_gene_variant 0.13
pepQ 2860585 c.-167G>T upstream_gene_variant 0.11
pepQ 2860589 c.-171G>A upstream_gene_variant 0.75
ribD 2987298 p.Gln154Lys missense_variant 0.11
ribD 2987378 c.540C>T synonymous_variant 0.14
Rv2752c 3066294 c.-103C>T upstream_gene_variant 0.14
Rv2752c 3066323 c.-132G>A upstream_gene_variant 0.11
Rv2752c 3066326 c.-135C>A upstream_gene_variant 0.12
Rv2752c 3067011 c.-820C>T upstream_gene_variant 0.17
Rv2752c 3067031 c.-840G>A upstream_gene_variant 0.17
Rv2752c 3067042 c.-851C>A upstream_gene_variant 0.19
Rv2752c 3067081 c.-890T>A upstream_gene_variant 0.1
thyX 3067851 p.Gly32Val missense_variant 0.11
thyX 3067993 c.-48C>A upstream_gene_variant 0.67
thyA 3074520 c.-49G>T upstream_gene_variant 0.12
thyA 3074523 c.-52G>A upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087326 c.507C>T synonymous_variant 0.25
ald 3087345 p.Ala176Ser missense_variant 0.1
fbiD 3339048 c.-70C>T upstream_gene_variant 0.12
fbiD 3339308 p.Pro64Gln missense_variant 0.14
fbiD 3339319 p.Ala68Thr missense_variant 0.18
fbiD 3339339 c.222G>T synonymous_variant 0.21
fbiD 3339549 c.432T>A synonymous_variant 0.11
fbiD 3339554 p.Thr146Asn missense_variant 0.11
fbiD 3339556 p.Gly147Ser missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474922 p.Asp306Asn missense_variant 0.13
Rv3236c 3612137 p.Gly327Val missense_variant 0.12
Rv3236c 3612171 p.Glu316* stop_gained 0.15
Rv3236c 3612177 c.940C>A synonymous_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 0.97
fbiB 3640767 c.-768C>T upstream_gene_variant 0.1
fbiA 3641222 p.Pro227His missense_variant 0.12
fbiB 3641633 c.99C>A synonymous_variant 0.14
fbiB 3642392 c.858G>T synonymous_variant 0.17
fbiB 3642394 p.Pro287Leu missense_variant 0.12
fbiB 3642411 p.Arg293Trp missense_variant 0.11
fbiB 3642660 p.Ala376Thr missense_variant 0.11
fbiB 3642663 p.Val377Ile missense_variant 0.13
alr 3840966 p.Ala152Val missense_variant 0.11
alr 3841226 c.195C>A synonymous_variant 0.14
clpC1 4038186 p.Ala840Val missense_variant 0.14
clpC1 4038222 p.Ala828Asp missense_variant 0.1
clpC1 4040226 p.Gly160Val missense_variant 0.11
panD 4044470 c.-189C>T upstream_gene_variant 0.11
panD 4044478 c.-197G>T upstream_gene_variant 0.25
embC 4240572 p.Gly237Glu missense_variant 0.2
embC 4240641 p.Arg260Leu missense_variant 0.18
embC 4240643 p.Arg261Leu missense_variant 0.14
embC 4240999 p.Trp379* stop_gained 0.1
embC 4241002 c.1140G>A synonymous_variant 0.14
embC 4241102 p.Glu414Lys missense_variant 0.13
embC 4241681 p.Ala607Thr missense_variant 0.27
embC 4241696 p.Ala612Ser missense_variant 0.13
embC 4242183 p.Ala774Val missense_variant 0.18
embC 4242195 p.Gly778Val missense_variant 0.12
embC 4242323 p.Gly821Asn missense_variant 0.1
embC 4242336 p.Gly825Asp missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242761 p.Arg967Trp missense_variant 0.14
embA 4243171 c.-62C>T upstream_gene_variant 0.12
embA 4243190 c.-43G>T upstream_gene_variant 0.1
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243554 p.Arg108Ser missense_variant 0.25
embA 4243630 p.Ala133Val missense_variant 0.13
embA 4243634 c.402A>T synonymous_variant 0.11
embA 4243896 p.Ala222Asn missense_variant 0.21
embA 4244211 p.Pro327Thr missense_variant 0.1
embA 4244221 p.Leu330Gln missense_variant 0.18
embA 4244432 c.1200C>A synonymous_variant 0.13
embA 4244601 p.Ala457Ser missense_variant 0.21
embA 4244840 c.1608G>A synonymous_variant 0.12
embA 4245437 p.Met735Ile missense_variant 0.16
embA 4245444 p.Asp738Asn missense_variant 0.12
embB 4245515 c.-999C>T upstream_gene_variant 0.12
embB 4245821 c.-693C>T upstream_gene_variant 0.13
embB 4246651 c.138G>A synonymous_variant 0.33
embB 4246800 p.Gly96Val missense_variant 0.22
embB 4247022 p.Ala170Glu missense_variant 0.12
embB 4247028 p.Leu172Arg missense_variant 0.25
embB 4247128 c.615C>T synonymous_variant 0.17
embB 4247298 p.Pro262Leu missense_variant 0.11
embB 4247672 p.Ala387Ser missense_variant 0.13
embB 4247832 p.Phe440Tyr missense_variant 0.12
embB 4247916 p.Arg468Leu missense_variant 0.22
embB 4247921 p.His470Tyr missense_variant 0.11
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4248588 p.Gly692Asp missense_variant 0.17
embB 4248591 p.Ala693Asp missense_variant 0.4
embB 4248629 p.Pro706Ser missense_variant 0.1
embB 4249169 p.Asn886His missense_variant 0.94
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267907 c.930C>T synonymous_variant 0.12
aftB 4267966 p.Arg291Ser missense_variant 0.17
aftB 4267982 c.855C>A synonymous_variant 0.15
aftB 4268468 c.369G>T synonymous_variant 0.11
aftB 4268475 p.Gly121Val missense_variant 0.1
aftB 4268485 p.Leu118Ile missense_variant 0.12
aftB 4268885 c.-49C>A upstream_gene_variant 0.5
aftB 4268896 c.-60G>A upstream_gene_variant 0.12
ubiA 4269716 c.106_117delCCGCTGGCCGCG conservative_inframe_deletion 0.18
ethA 4326891 p.Ala195Thr missense_variant 0.11
ethA 4327599 c.-126G>T upstream_gene_variant 0.12
ethR 4327600 p.Ala18Thr missense_variant 0.11
ethA 4328023 c.-550G>T upstream_gene_variant 0.14
ethA 4328028 c.-555G>T upstream_gene_variant 0.15
ethA 4328046 c.-573C>A upstream_gene_variant 0.17
ethR 4328047 p.Pro167Ser missense_variant 0.12
ethA 4328421 c.-948G>T upstream_gene_variant 0.11
whiB6 4338194 p.Arg110Trp missense_variant 0.12
whiB6 4338201 c.321C>T synonymous_variant 0.11
whiB6 4338207 c.315G>T synonymous_variant 0.15
whiB6 4338313 p.Ala70Val missense_variant 0.5
whiB6 4338334 p.Ala63Glu missense_variant 0.13
whiB6 4338345 c.177G>A synonymous_variant 0.1
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408104 c.99G>T synonymous_variant 0.1
gid 4408316 c.-114C>A upstream_gene_variant 0.12