TB-Profiler result

Run: ERR3994115
Summary

Run ID: ERR3994115

Sample name:

Date: 01-04-2023 03:43:00

Number of reads: 3975547

Percentage reads mapped: 99.99

Strain: lineage2.2.1

Drug-resistance: Sensitive

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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
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
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 5753 p.Arg172Trp missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7607 c.306C>A synonymous_variant 0.17
gyrA 7671 p.Pro124Ser missense_variant 0.13
gyrA 9286 p.Ala662Gly missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491272 p.Asp164His missense_variant 0.12
fgd1 491283 p.Asp167Glu missense_variant 0.14
fgd1 491311 p.Gly177Cys missense_variant 0.14
fgd1 491326 p.Ala182Pro missense_variant 0.15
fgd1 491529 p.Trp249Cys missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575431 c.84C>G synonymous_variant 0.12
mshA 575720 p.Leu125Met missense_variant 0.17
mshA 575780 p.Pro145Thr missense_variant 0.14
mshA 575867 p.Val174Leu missense_variant 0.13
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576119 p.Ala258Ser missense_variant 0.22
mshA 576151 c.804G>T synonymous_variant 0.14
ccsA 619713 c.-178C>A upstream_gene_variant 0.18
ccsA 619734 c.-157C>A upstream_gene_variant 0.2
ccsA 619886 c.-5G>T upstream_gene_variant 0.15
ccsA 620164 p.Leu92Met missense_variant 0.15
ccsA 620351 p.Arg154Leu missense_variant 0.15
ccsA 620505 p.Glu205Asp missense_variant 0.18
ccsA 620507 p.Pro206Arg missense_variant 0.18
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761257 p.Glu484Val missense_variant 0.14
rpoB 761525 p.Met573Ile missense_variant 0.11
rpoB 762562 p.Arg919Pro missense_variant 0.13
rpoB 762589 p.Thr928Ser missense_variant 0.12
rpoB 762761 p.Cys985* stop_gained 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763939 p.Lys190Asn missense_variant 0.12
rpoC 764065 p.Lys232Asn missense_variant 0.17
rpoC 764596 p.Lys409Asn missense_variant 0.13
rpoC 764890 p.Leu507Phe missense_variant 0.11
rpoC 765157 c.1788C>A synonymous_variant 0.14
rpoC 765295 c.1926G>A synonymous_variant 0.13
rpoC 765342 p.Pro658Arg missense_variant 0.12
rpoC 765762 p.Pro798Gln missense_variant 0.17
rpoC 765822 p.Ala818Asp missense_variant 0.14
rpoC 765825 p.Gly819Ala missense_variant 0.14
rpoC 765833 p.Gly822Cys missense_variant 0.14
rpoC 766279 c.2910C>G synonymous_variant 0.12
rpoC 766364 p.Ala999Pro missense_variant 0.13
rpoC 766645 p.Glu1092Asp missense_variant 1.0
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 776303 c.2178G>C synonymous_variant 0.12
mmpL5 777709 p.Leu258Phe missense_variant 0.13
mmpL5 777766 p.Gly239Arg missense_variant 0.15
mmpL5 777890 p.Gln197His missense_variant 0.14
mmpL5 778010 p.Gln157His missense_variant 0.2
mmpL5 779472 c.-992G>T upstream_gene_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406111 p.Asp410Glu missense_variant 0.18
Rv1258c 1406693 c.648G>T synonymous_variant 0.14
Rv1258c 1406709 p.Gly211Val missense_variant 0.14
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407495 c.-155C>A upstream_gene_variant 0.33
embR 1416821 p.Ala176Asp missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472184 n.339T>C non_coding_transcript_exon_variant 0.25
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.28
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 0.22
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.2
rrl 1475859 n.2202G>T non_coding_transcript_exon_variant 0.13
inhA 1673766 c.-436C>A upstream_gene_variant 0.14
inhA 1674873 p.Gln224His missense_variant 0.14
inhA 1674925 p.Val242Leu missense_variant 0.13
inhA 1674932 p.Ala244Gly missense_variant 0.12
rpsA 1833409 c.-133C>T upstream_gene_variant 1.0
rpsA 1833420 c.-122C>G upstream_gene_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834980 p.Ser480Ile missense_variant 0.14
tlyA 1917769 c.-171C>A upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918674 c.735G>C synonymous_variant 0.17
tlyA 1918734 p.Ser265Arg missense_variant 0.15
ndh 2102139 p.Arg302Gly missense_variant 0.17
ndh 2102146 c.897G>C synonymous_variant 0.17
ndh 2102292 p.Asp251Asn missense_variant 0.25
ndh 2102358 p.Gly229Arg missense_variant 0.17
ndh 2102380 c.663G>T synonymous_variant 0.14
ndh 2102423 p.Thr207Ser missense_variant 0.18
katG 2153900 p.Asp738Asn missense_variant 0.15
katG 2154563 p.Val517Leu missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155217 p.Gly299Arg missense_variant 0.18
katG 2155317 c.795G>T synonymous_variant 0.18
katG 2155477 p.Gly212Asp missense_variant 0.18
katG 2155693 p.Ser140Ile missense_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169941 c.672C>A synonymous_variant 0.18
PPE35 2170381 p.Ala78Thr missense_variant 0.14
PPE35 2170472 c.141G>C synonymous_variant 0.15
PPE35 2170623 c.-11G>A upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290204 c.-963G>T upstream_gene_variant 0.13
kasA 2518737 p.Ala208Glu missense_variant 0.15
kasA 2519077 c.963G>C synonymous_variant 0.22
eis 2714248 p.Gly362Ala missense_variant 0.22
eis 2714955 c.378C>T synonymous_variant 1.0
eis 2715037 p.Ala99Val missense_variant 0.13
eis 2715433 c.-101T>C upstream_gene_variant 0.11
folC 2746317 p.Asp428Asn missense_variant 0.17
folC 2746366 c.1233G>T synonymous_variant 0.18
folC 2746511 p.Ala363Glu missense_variant 0.2
folC 2746648 c.951G>T synonymous_variant 0.15
folC 2746696 p.Asn301Lys missense_variant 0.15
folC 2746960 c.639C>A synonymous_variant 0.18
folC 2747775 c.-177C>G upstream_gene_variant 0.17
pepQ 2859759 p.Ile220Met missense_variant 0.12
ribD 2986669 c.-170G>T upstream_gene_variant 0.17
ribD 2987056 p.Leu73Arg missense_variant 0.13
ribD 2987120 c.282C>T synonymous_variant 0.15
ribD 2987132 p.Met98Ile missense_variant 0.17
ribD 2987184 p.Gln116Lys missense_variant 0.17
ribD 2987354 c.516G>C synonymous_variant 0.15
ribD 2987367 p.Val177Leu missense_variant 0.18
ribD 2987535 p.Gln233Glu missense_variant 0.25
ribD 2987582 c.744C>G synonymous_variant 0.15
Rv2752c 3066197 c.-6C>T upstream_gene_variant 0.14
Rv2752c 3066261 c.-70G>C upstream_gene_variant 0.15
Rv2752c 3066337 c.-146G>T upstream_gene_variant 0.17
thyX 3067907 c.39C>G synonymous_variant 0.14
thyX 3067948 c.-3G>C upstream_gene_variant 0.15
thyA 3074049 p.Met141Ile missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339139 p.Gly8Arg missense_variant 0.4
fbiD 3339630 c.513C>T synonymous_variant 1.0
Rv3083 3449004 p.Gln167His missense_variant 0.15
Rv3083 3449149 p.Tyr216His missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474049 p.Ala15Pro missense_variant 0.12
Rv3236c 3612007 c.1110C>A synonymous_variant 0.2
Rv3236c 3612025 c.1092C>A synonymous_variant 0.2
Rv3236c 3612070 c.1047G>T synonymous_variant 0.15
Rv3236c 3612083 p.Gly345Ala missense_variant 0.17
Rv3236c 3612152 p.Gly322Val missense_variant 0.25
Rv3236c 3612201 p.Val306Leu missense_variant 0.14
Rv3236c 3612346 p.Asp257Glu missense_variant 0.18
Rv3236c 3612617 p.Pro167Gln missense_variant 0.15
Rv3236c 3612692 p.Arg142Gln missense_variant 0.17
Rv3236c 3612715 c.402G>T synonymous_variant 0.2
Rv3236c 3612748 c.369G>T synonymous_variant 0.22
Rv3236c 3612783 p.Gly112Trp missense_variant 0.2
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3640617 c.-918G>T upstream_gene_variant 0.14
fbiA 3641030 p.Ser163Thr missense_variant 0.13
fbiA 3641072 p.Arg177Pro missense_variant 0.15
fbiB 3641121 c.-414C>G upstream_gene_variant 0.17
fbiA 3641125 p.Ala195Pro missense_variant 0.17
fbiA 3641128 p.Ala196Ser missense_variant 0.17
fbiA 3641146 p.Ala202Pro missense_variant 0.14
fbiA 3641172 p.Met210Ile missense_variant 0.14
fbiB 3641858 c.324G>T synonymous_variant 0.13
fbiB 3642621 p.Ala363Ser missense_variant 0.29
fbiB 3642728 p.Ile398Met missense_variant 0.33
fbiB 3642872 p.Ile446Met missense_variant 0.12
alr 3841200 p.Ala74Asp missense_variant 0.17
rpoA 3877802 p.Pro236Ala missense_variant 0.11
rpoA 3878049 c.459G>T synonymous_variant 0.13
rpoA 3878078 p.Arg144Ser missense_variant 0.18
rpoA 3878090 p.Val140Leu missense_variant 0.18
rpoA 3878099 p.Glu137* stop_gained 0.2
rpoA 3878544 c.-37C>G upstream_gene_variant 0.2
rpoA 3878700 c.-193C>G upstream_gene_variant 0.13
clpC1 4038227 c.2478G>T synonymous_variant 0.14
clpC1 4039273 p.Glu478Gln missense_variant 0.12
clpC1 4040265 p.Gly147Ala missense_variant 0.12
panD 4043918 p.Ala122Pro missense_variant 0.11
panD 4044391 c.-111delG upstream_gene_variant 0.13
panD 4044397 c.-116G>C upstream_gene_variant 0.13
embC 4239701 c.-162C>A upstream_gene_variant 0.22
embC 4239848 c.-15G>C upstream_gene_variant 0.15
embC 4240290 p.Pro143Arg missense_variant 0.11
embC 4240333 p.Phe157Leu missense_variant 0.14
embC 4240465 p.Phe201Leu missense_variant 0.25
embC 4240634 p.Arg258Trp missense_variant 0.18
embC 4240822 c.960C>A synonymous_variant 0.13
embC 4241327 p.Arg489Ser missense_variant 0.33
embC 4242223 c.2361C>A synonymous_variant 0.15
embC 4242286 p.Phe808Leu missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243007 p.Leu1049Ile missense_variant 0.17
embA 4243255 p.Arg8Pro missense_variant 0.15
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243969 p.Val246Ala missense_variant 0.13
embA 4244222 c.990G>T synonymous_variant 0.29
embA 4244371 p.Arg380Leu missense_variant 0.18
embA 4244400 p.Leu390Met missense_variant 0.22
embA 4244419 c.1189dupG frameshift_variant 0.22
embA 4244501 c.1269G>T synonymous_variant 0.29
embA 4244660 c.1428G>T synonymous_variant 0.15
embA 4245473 c.2241C>G synonymous_variant 0.15
embA 4245513 p.Asp761Asn missense_variant 0.14
embB 4245527 c.-987C>A upstream_gene_variant 0.14
embA 4245975 p.Asp915His missense_variant 0.13
embA 4246007 c.2776delC frameshift_variant 0.12
embA 4246038 p.Ala936Pro missense_variant 0.12
embA 4246170 p.Asp980Tyr missense_variant 0.15
embA 4246289 p.Asn1019Lys missense_variant 0.15
embA 4246509 p.Leu1093Ile missense_variant 0.14
embB 4246767 p.Cys85Phe missense_variant 0.13
embB 4247001 p.Gly163Val missense_variant 0.2
embB 4248956 p.Trp815Gly missense_variant 0.14
embB 4248964 c.2451G>C synonymous_variant 0.12
embB 4249045 p.Leu844Phe missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267708 p.Gly377Arg missense_variant 0.2
aftB 4267710 p.Ser376Ile missense_variant 0.2
aftB 4268127 p.Pro237Gln missense_variant 0.14
aftB 4268149 p.Gly230Cys missense_variant 0.15
aftB 4268176 p.Pro221Ala missense_variant 0.17
aftB 4268517 p.Ala107Glu missense_variant 0.13
aftB 4268695 p.Val48Leu missense_variant 0.13
aftB 4268701 p.Gly46Arg missense_variant 0.13
aftB 4268783 c.54C>A synonymous_variant 0.13
ubiA 4269120 p.Phe238Leu missense_variant 0.25
aftB 4269564 c.-728G>C upstream_gene_variant 0.18
ethR 4328026 p.Gly160Ser missense_variant 0.14
ethR 4328047 p.Pro167Thr missense_variant 0.15
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 4408215 c.-13G>T upstream_gene_variant 0.17
gid 4408465 c.-263C>G upstream_gene_variant 0.12