TB-Profiler result

Run: SRR1173380
Summary

Run ID: SRR1173380

Sample name:

Date: 03-04-2023 03:23:20

Number of reads: 1130167

Percentage reads mapped: 32.58

Strain: lineage3;lineage2.2

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
lineage3 East-African-Indian CAS RD750 0.73
lineage2 East-Asian Beijing RD105 0.28
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.28
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 7582 p.Asp94Ala missense_variant 0.73 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.16 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.36 isoniazid
katG 2155700 p.Asn138His missense_variant 0.62 isoniazid
pncA 2288883 p.Leu120Pro missense_variant 0.42 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 0.35 kanamycin
embB 4249518 p.His1002Arg missense_variant 0.79 ethambutol
ethA 4326183 c.1290delC frameshift_variant 0.26 ethionamide, ethionamide
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 575268 c.-80C>A upstream_gene_variant 0.22
mshA 575907 p.Ala187Val missense_variant 0.28
ccsA 620625 p.Ile245Met missense_variant 0.37
rpoB 759746 c.-61C>T upstream_gene_variant 0.6
rpoB 760461 p.Arg219Cys missense_variant 0.25
rpoB 761035 p.Thr410Arg missense_variant 0.11
rpoB 761292 p.Val496Met missense_variant 0.83
rpoB 761634 p.Val610Leu missense_variant 0.17
rpoB 761852 c.2046C>A synonymous_variant 0.14
rpoC 762434 c.-936T>G upstream_gene_variant 0.82
rpoC 762710 c.-660G>T upstream_gene_variant 0.14
rpoB 762783 p.Asp993Tyr missense_variant 0.14
rpoB 762998 p.Glu1064Asp missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.42
mmpS5 779615 c.-710C>G upstream_gene_variant 0.38
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302940 p.Pro4Thr missense_variant 0.33
Rv1258c 1406939 c.402G>T synonymous_variant 0.21
embR 1416631 c.717C>A synonymous_variant 0.14
embR 1416634 p.Asp238Glu missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.3
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.31
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.4
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.42
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.58
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.63
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.66
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.63
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.58
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.65
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.58
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.58
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.56
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.61
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.29
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.42
rrs 1472553 n.708C>T non_coding_transcript_exon_variant 0.47
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.6
rrs 1472572 n.727T>C non_coding_transcript_exon_variant 0.5
rrs 1472574 n.729T>C non_coding_transcript_exon_variant 0.5
rrs 1472579 n.734G>A non_coding_transcript_exon_variant 0.52
rrs 1472582 n.737G>A non_coding_transcript_exon_variant 0.47
rrs 1472583 n.738T>A non_coding_transcript_exon_variant 0.46
rrs 1472584 n.739A>G non_coding_transcript_exon_variant 0.47
rrs 1472594 n.749G>C non_coding_transcript_exon_variant 0.48
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.6
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.58
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.23
rrs 1472714 n.869A>C non_coding_transcript_exon_variant 0.27
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 0.26
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.3
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.86
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.82
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.83
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.81
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.14
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.11
rrs 1473139 n.1294T>C non_coding_transcript_exon_variant 0.28
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.44
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.52
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.67
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.7
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.66
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.67
rrs 1473198 n.1354delC non_coding_transcript_exon_variant 0.67
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.66
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.66
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.14
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.42
rrl 1475538 n.1881T>C non_coding_transcript_exon_variant 0.4
rrl 1475539 n.1882A>T non_coding_transcript_exon_variant 0.4
rrl 1475540 n.1883C>T non_coding_transcript_exon_variant 0.4
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.39
rrl 1475550 n.1893A>C non_coding_transcript_exon_variant 0.4
rrl 1475551 n.1894T>G non_coding_transcript_exon_variant 0.4
rrl 1475555 n.1898T>G non_coding_transcript_exon_variant 0.41
rrl 1475564 n.1907C>A non_coding_transcript_exon_variant 0.42
rrl 1475574 n.1917C>G non_coding_transcript_exon_variant 0.42
rrl 1475575 n.1918C>T non_coding_transcript_exon_variant 0.42
rrl 1475576 n.1919C>G non_coding_transcript_exon_variant 0.42
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.11
rrl 1476312 n.2655T>C 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 0.69
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.7
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.7
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.82
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.7
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.86
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.12
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.72
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.85
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.83
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.72
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.91
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.77
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.87
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.84
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.13
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.7
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.71
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.72
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.75
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.72
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.79
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.52
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.33
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.19
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 0.42
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917996 c.57A>G synonymous_variant 0.14
tlyA 1918714 p.Ala259Ser missense_variant 0.14
ndh 2102154 p.Leu297Val missense_variant 0.14
ndh 2102161 c.882G>T synonymous_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155832 p.Asp94His missense_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.42
PPE35 2170086 p.Ala176Glu missense_variant 0.18
PPE35 2170342 p.Gln91* stop_gained 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.75
pncA 2290122 c.-881A>G upstream_gene_variant 0.17
eis 2714370 c.963C>A synonymous_variant 0.15
ahpC 2726105 c.-88G>A upstream_gene_variant 0.69
ahpC 2726117 c.-76T>A upstream_gene_variant 0.61
pepQ 2860159 p.Ala87Asp missense_variant 0.15
Rv2752c 3065940 p.Glu84Asp missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474352 p.Gly116Ser missense_variant 0.13
Rv3236c 3612756 p.Leu121Met missense_variant 0.15
Rv3236c 3612813 p.Thr102Ala missense_variant 0.2
fbiB 3642731 c.1197C>A synonymous_variant 0.15
fbiB 3642877 p.Lys448Arg missense_variant 0.78
alr 3840554 c.867G>T synonymous_variant 0.15
alr 3841403 p.Glu6Asp missense_variant 0.19
clpC1 4038935 c.1770C>T synonymous_variant 0.15
clpC1 4040083 p.Thr208Ser missense_variant 0.12
clpC1 4040894 c.-190G>A upstream_gene_variant 0.17
clpC1 4040904 c.-200G>A upstream_gene_variant 0.14
embC 4240540 c.678C>A synonymous_variant 0.13
embC 4241102 c.1244_1260delGGGCGGTGGCCACCAGC frameshift_variant 0.17
embC 4241127 c.1267_1272delCTGCCG conservative_inframe_deletion 0.2
embC 4242075 p.Arg738Gln missense_variant 0.77
embC 4242582 p.Ala907Val missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.33
embA 4243612 p.Ala127Asp missense_variant 0.14
embA 4244945 c.1713C>A synonymous_variant 0.12
embB 4247965 c.1452C>T synonymous_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 0.23
aftB 4267832 c.1005C>T synonymous_variant 0.12
aftB 4268506 p.Arg111Trp missense_variant 0.22
aftB 4269156 c.-320C>T upstream_gene_variant 0.14
whiB6 4338563 c.-42G>T upstream_gene_variant 0.32
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.38