TB-Profiler result

Run: SRR1173343
Summary

Run ID: SRR1173343

Sample name:

Date: 03-04-2023 03:22:22

Number of reads: 908604

Percentage reads mapped: 26.43

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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620855 p.Gly322Asp missense_variant 0.2
rpoB 760589 c.783C>T synonymous_variant 0.12
rpoB 761051 c.1245G>A synonymous_variant 0.22
rpoB 761064 p.Ala420Thr missense_variant 0.2
rpoB 761364 p.Asp520Tyr missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763448 p.Glu27Lys missense_variant 0.14
rpoC 765253 p.Ser628Arg missense_variant 0.2
rpoC 766577 p.Asp1070Asn missense_variant 0.15
rpoC 766976 p.Gly1203Ser missense_variant 0.14
rpoC 767259 p.Phe1297Tyr missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.96
mmpL5 777367 p.Arg372Trp missense_variant 0.18
mmpL5 778923 c.-443C>T upstream_gene_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781552 c.-8G>A upstream_gene_variant 0.12
rpsL 781580 c.21G>A synonymous_variant 0.14
Rv1258c 1406740 p.His201Asn missense_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472135 n.290C>T non_coding_transcript_exon_variant 0.2
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.19
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.32
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.42
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.47
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.56
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.57
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.59
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.58
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.55
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.42
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.42
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.43
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.43
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.44
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.25
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.25
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.26
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.2
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.17
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.17
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.17
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.22
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.31
rrs 1472553 n.708C>T non_coding_transcript_exon_variant 0.45
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.38
rrs 1472572 n.727T>C non_coding_transcript_exon_variant 0.39
rrs 1472574 n.729T>C non_coding_transcript_exon_variant 0.37
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.37
rrs 1472582 n.737G>A non_coding_transcript_exon_variant 0.37
rrs 1472583 n.738T>A non_coding_transcript_exon_variant 0.37
rrs 1472584 n.739A>G non_coding_transcript_exon_variant 0.37
rrs 1472594 n.749G>C non_coding_transcript_exon_variant 0.42
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.44
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.44
rrs 1472697 n.852T>G non_coding_transcript_exon_variant 0.22
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.31
rrs 1472714 n.869A>C non_coding_transcript_exon_variant 0.32
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.33
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.35
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.81
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.81
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.82
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.8
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.17
rrs 1473139 n.1294T>C non_coding_transcript_exon_variant 0.33
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.52
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.62
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.75
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.75
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.76
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.78
rrs 1473198 n.1354delC non_coding_transcript_exon_variant 0.8
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.78
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.78
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.37
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.22
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.14
rrl 1475133 n.1476C>A non_coding_transcript_exon_variant 0.22
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.49
rrl 1475538 n.1881T>C non_coding_transcript_exon_variant 0.48
rrl 1475539 n.1882A>T non_coding_transcript_exon_variant 0.48
rrl 1475540 n.1883C>T non_coding_transcript_exon_variant 0.48
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.48
rrl 1475550 n.1893A>C non_coding_transcript_exon_variant 0.48
rrl 1475551 n.1894T>G non_coding_transcript_exon_variant 0.48
rrl 1475555 n.1898T>G non_coding_transcript_exon_variant 0.48
rrl 1475564 n.1907C>A non_coding_transcript_exon_variant 0.5
rrl 1475574 n.1917C>G non_coding_transcript_exon_variant 0.52
rrl 1475575 n.1918C>T non_coding_transcript_exon_variant 0.52
rrl 1475576 n.1919C>G non_coding_transcript_exon_variant 0.52
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.11
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.11
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.14
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.58
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.74
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.73
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.73
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.74
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.77
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.77
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.78
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.76
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.76
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.81
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.81
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.83
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.83
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.79
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.8
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>T non_coding_transcript_exon_variant 0.79
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.79
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.65
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.49
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.26
rpsA 1833619 c.78A>C synonymous_variant 0.11
rpsA 1833955 c.414G>A synonymous_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834788 p.Ala416Asp missense_variant 0.12
rpsA 1834926 p.Gly462Val missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918299 p.Trp120* stop_gained 0.18
ndh 2102589 c.454T>C synonymous_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 0.96
katG 2155193 p.Gly307* stop_gained 0.13
katG 2155779 c.333C>A synonymous_variant 0.4
PPE35 2167926 p.Leu896Ser missense_variant 0.95
PPE35 2169320 p.Leu431Phe missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290170 c.-930dupG upstream_gene_variant 0.13
pncA 2290174 c.-933A>G upstream_gene_variant 0.13
kasA 2518534 c.420G>A synonymous_variant 0.4
kasA 2518792 c.678C>A synonymous_variant 0.12
folC 2746790 p.Ile270Asn missense_variant 0.2
folC 2747750 c.-152G>T upstream_gene_variant 0.12
pepQ 2859416 p.Gly335Cys missense_variant 0.17
Rv2752c 3064772 p.Ala474Thr missense_variant 0.2
Rv2752c 3065716 c.474_475delGT frameshift_variant 0.14
thyA 3073860 c.612C>T synonymous_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087898 p.Gly360Val missense_variant 0.22
ald 3087900 p.Val361Leu missense_variant 0.22
fbiD 3338959 c.-159C>G upstream_gene_variant 0.12
fbiD 3339592 p.His159Tyr missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474352 p.Gly116Arg missense_variant 0.22
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613163 c.-47G>T upstream_gene_variant 0.12
fbiA 3640609 p.Leu23Phe missense_variant 0.12
fbiB 3642123 p.Glu197* stop_gained 0.13
fbiB 3642359 c.825C>A synonymous_variant 0.15
alr 3840552 p.Gly290Val missense_variant 0.15
rpoA 3877817 p.Gly231Cys missense_variant 0.17
ddn 3986738 c.-106C>A upstream_gene_variant 0.14
clpC1 4038255 p.Val817Lys missense_variant 0.17
clpC1 4038271 p.Pro812Ala missense_variant 0.12
clpC1 4038272 p.Gly811Ser missense_variant 0.12
clpC1 4038275 c.2430A>G synonymous_variant 0.12
clpC1 4038278 c.2427T>C synonymous_variant 0.12
clpC1 4038293 c.2412G>C synonymous_variant 0.14
clpC1 4039610 c.1095G>C synonymous_variant 0.12
clpC1 4039616 c.1089G>C synonymous_variant 0.13
clpC1 4039622 c.1083C>T synonymous_variant 0.12
clpC1 4039649 c.1056G>C synonymous_variant 0.15
clpC1 4039652 c.1053G>C synonymous_variant 0.15
clpC1 4039670 c.1035G>C synonymous_variant 0.12
embC 4240654 c.792C>A synonymous_variant 0.22
embA 4242352 c.-881G>T upstream_gene_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243112 p.Gly1084Arg missense_variant 0.12
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245407 c.2175G>T synonymous_variant 0.22
embA 4245857 c.2626delG frameshift_variant 0.14
embB 4249757 p.Thr1082Ala missense_variant 0.89
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268445 p.Ala131Asp missense_variant 0.13
aftB 4268476 p.Gly121Trp missense_variant 0.18
ubiA 4269239 p.Ala199Ser missense_variant 0.14
ubiA 4269864 c.-31C>A upstream_gene_variant 0.13
ethA 4326821 p.Arg218Leu missense_variant 0.22
whiB6 4338239 p.Leu95Val missense_variant 0.22
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 4408465 c.-263C>A upstream_gene_variant 0.15