TB-Profiler result

Run: SRR1174277
Summary

Run ID: SRR1174277

Sample name:

Date: 03-04-2023 03:33:40

Number of reads: 736342

Percentage reads mapped: 25.46

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-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
lineage2 East-Asian Beijing RD105 1.0
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
gyrA 7572 p.Ser91Pro missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247729 p.Gly406Ser missense_variant 1.0 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 7443 p.Leu48Ile missense_variant 0.18
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8540 c.1239C>G synonymous_variant 0.12
gyrA 8542 c.1242_1243insTCC conservative_inframe_insertion 0.13
gyrA 8591 c.1290C>A synonymous_variant 0.17
gyrA 9107 c.1806C>T synonymous_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.94
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576242 p.Gly299Cys missense_variant 0.15
ccsA 620261 p.Ala124Val missense_variant 0.22
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759993 p.Arg63Cys missense_variant 0.17
rpoB 760358 c.552C>A synonymous_variant 0.12
rpoB 761194 p.Gly463Val missense_variant 0.17
rpoB 762018 p.Glu738* stop_gained 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763604 p.Gly79Cys missense_variant 0.17
rpoC 763615 c.246G>T synonymous_variant 0.14
rpoC 765119 p.Gly584Arg missense_variant 0.15
rpoC 765136 c.1767C>A synonymous_variant 0.2
rpoC 766658 p.Arg1097Trp missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.91
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpR5 778022 c.-968G>A upstream_gene_variant 0.17
mmpL5 778063 p.Gln140* stop_gained 0.15
mmpR5 778121 c.-869G>A upstream_gene_variant 0.22
mmpS5 778518 p.Gly130Ser missense_variant 0.29
mmpS5 779615 c.-710C>G upstream_gene_variant 0.94
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801278 p.Pro157Leu missense_variant 0.15
fbiC 1303369 p.Leu147Ile missense_variant 0.12
Rv1258c 1406421 p.Phe307Ser missense_variant 0.15
Rv1258c 1406726 c.615C>T synonymous_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 0.8
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472135 n.290C>T non_coding_transcript_exon_variant 0.12
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.38
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.46
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.52
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.53
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.6
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.63
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.65
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.64
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.63
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.58
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.58
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.56
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.56
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.56
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.17
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.25
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.24
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.15
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.27
rrs 1472553 n.708C>T non_coding_transcript_exon_variant 0.29
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.29
rrs 1472572 n.727T>C non_coding_transcript_exon_variant 0.28
rrs 1472574 n.729T>C non_coding_transcript_exon_variant 0.29
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.29
rrs 1472582 n.737G>A non_coding_transcript_exon_variant 0.29
rrs 1472583 n.738T>A non_coding_transcript_exon_variant 0.29
rrs 1472584 n.739A>G non_coding_transcript_exon_variant 0.29
rrs 1472594 n.749G>C non_coding_transcript_exon_variant 0.32
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.31
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.33
rrs 1472697 n.852T>G non_coding_transcript_exon_variant 0.2
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.45
rrs 1472714 n.869A>C non_coding_transcript_exon_variant 0.45
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.45
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.47
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.83
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.83
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.81
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.8
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.14
rrs 1473139 n.1294T>C non_coding_transcript_exon_variant 0.37
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.47
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.54
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.66
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.66
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.67
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.74
rrs 1473198 n.1354delC non_coding_transcript_exon_variant 0.71
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.72
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.74
rrl 1475145 n.1488C>A non_coding_transcript_exon_variant 0.25
rrl 1475491 n.1834C>T non_coding_transcript_exon_variant 0.13
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.67
rrl 1475538 n.1881T>C non_coding_transcript_exon_variant 0.68
rrl 1475539 n.1882A>T non_coding_transcript_exon_variant 0.68
rrl 1475540 n.1883C>T non_coding_transcript_exon_variant 0.68
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.68
rrl 1475550 n.1893A>C non_coding_transcript_exon_variant 0.68
rrl 1475551 n.1894T>G non_coding_transcript_exon_variant 0.7
rrl 1475555 n.1898T>G non_coding_transcript_exon_variant 0.72
rrl 1475564 n.1907C>A non_coding_transcript_exon_variant 0.72
rrl 1475574 n.1917C>G non_coding_transcript_exon_variant 0.72
rrl 1475575 n.1918C>T non_coding_transcript_exon_variant 0.72
rrl 1475576 n.1919C>G non_coding_transcript_exon_variant 0.72
rrl 1475760 n.2105_2106delGC non_coding_transcript_exon_variant 0.12
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.12
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.79
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.79
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.78
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.78
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.78
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.82
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.81
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.82
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.83
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.83
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.9
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.89
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.88
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.88
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.87
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.86
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.85
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.85
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.84
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.84
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.5
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.38
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.14
rrl 1476545 n.2888C>G non_coding_transcript_exon_variant 0.12
inhA 1673574 c.-628C>A upstream_gene_variant 0.12
inhA 1673907 c.-295C>T upstream_gene_variant 0.18
rpsA 1833751 c.210C>T synonymous_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834348 c.807T>C synonymous_variant 0.15
rpsA 1834396 c.855G>A synonymous_variant 0.15
rpsA 1834958 p.Leu473Met missense_variant 0.2
rpsA 1834963 c.1422G>A synonymous_variant 0.18
tlyA 1917748 c.-192G>T upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918083 p.Asp48Glu missense_variant 0.29
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222862 c.303C>A synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290131 c.-890G>T upstream_gene_variant 0.17
kasA 2518442 p.Val110Phe missense_variant 0.12
kasA 2518670 p.Val186Met missense_variant 0.17
eis 2714198 p.Asp379Tyr missense_variant 0.15
eis 2714589 c.744G>A synonymous_variant 0.2
ahpC 2725916 c.-277C>A upstream_gene_variant 0.25
folC 2746878 p.Val241Ile missense_variant 0.14
folC 2747542 c.57C>A synonymous_variant 0.12
pepQ 2859604 p.Gly272Val missense_variant 0.22
pepQ 2859702 c.717G>A synonymous_variant 0.15
ribD 2987513 c.675C>A synonymous_variant 0.18
Rv2752c 3065707 p.Ala162Glu missense_variant 0.15
thyX 3067890 c.55delG frameshift_variant 0.29
thyA 3074336 p.Thr46Ser missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449207 p.Pro235Arg missense_variant 0.15
Rv3083 3449712 c.1209C>T synonymous_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475061 p.Pro352His missense_variant 0.18
fprA 3475234 c.1228C>T synonymous_variant 0.25
Rv3236c 3612077 p.Ser347* stop_gained 0.2
Rv3236c 3612273 p.Val282Ile missense_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642178 p.Ala215Glu missense_variant 0.33
alr 3841131 p.Ala97Glu missense_variant 0.17
alr 3841254 p.Ala56Asp missense_variant 0.2
rpoA 3878047 p.Ala154Asp missense_variant 0.17
rpoA 3878496 c.12A>G synonymous_variant 0.29
rpoA 3878666 c.-159C>T upstream_gene_variant 0.33
ddn 3986648 c.-196C>G upstream_gene_variant 0.18
ddn 3986665 c.-179G>C upstream_gene_variant 0.12
ddn 3987131 c.288C>A synonymous_variant 0.2
clpC1 4038892 p.Glu605* stop_gained 0.33
clpC1 4039636 p.Glu357* stop_gained 0.13
clpC1 4040528 c.177G>T synonymous_variant 0.22
embC 4241534 p.Pro558Ser missense_variant 0.17
embC 4242073 c.2211C>T synonymous_variant 0.12
embC 4242339 p.Thr826Asn missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243547 c.315G>A synonymous_variant 0.15
embA 4244297 c.1065G>A synonymous_variant 0.33
embA 4244915 c.1683G>T synonymous_variant 0.13
embA 4245071 c.1839G>T synonymous_variant 0.12
embA 4245088 c.1859delG frameshift_variant 0.17
embA 4245906 p.Leu892Met missense_variant 0.22
embB 4247626 c.1113C>A synonymous_variant 0.17
embB 4247916 p.Arg468Leu missense_variant 0.5
embB 4249757 p.Thr1082Ala missense_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268023 p.Leu272Met missense_variant 0.2
whiB6 4338207 c.315G>A synonymous_variant 0.29
whiB6 4338577 c.-56G>A upstream_gene_variant 0.14
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