TB-Profiler result

Run: SRR1013622
Summary

Run ID: SRR1013622

Sample name:

Date: 02-04-2023 15:59:30

Number of reads: 562196

Percentage reads mapped: 10.92

Strain: 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
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 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 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7572 p.Ser91Pro missense_variant 0.92 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.65 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155693 p.Ser140Asn missense_variant 0.8 isoniazid
pncA 2288839 p.Thr135Pro missense_variant 0.88 pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
ethA 4326643 c.820_830delGAGGGGTACGA frameshift_variant 1.0 ethionamide
gid 4408100 c.102delG frameshift_variant 1.0 streptomycin
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 491025 p.Tyr81* stop_gained 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759939 p.Pro45Ser missense_variant 0.2
rpoB 761645 c.1839C>T synonymous_variant 0.22
rpoB 761649 p.Ser615Ala missense_variant 0.22
rpoC 762893 c.-477C>T upstream_gene_variant 0.33
rpoC 762896 c.-474G>C upstream_gene_variant 0.42
rpoC 762917 c.-453C>G upstream_gene_variant 0.41
rpoC 762920 c.-450C>T upstream_gene_variant 0.4
rpoC 762923 c.-447C>G upstream_gene_variant 0.38
rpoB 762925 p.Thr1040Ile missense_variant 0.36
rpoC 762929 c.-441G>T upstream_gene_variant 0.38
rpoB 762939 p.Met1045Leu missense_variant 0.35
rpoB 762942 p.Ile1046Val missense_variant 0.35
rpoC 762965 c.-405T>C upstream_gene_variant 0.34
rpoC 762980 c.-390T>C upstream_gene_variant 0.37
rpoC 762989 c.-381G>C upstream_gene_variant 0.23
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764329 c.960C>T synonymous_variant 0.43
rpoC 764338 p.Glu323Asp missense_variant 0.5
rpoC 764344 c.975C>T synonymous_variant 0.48
rpoC 764348 p.Met327Leu missense_variant 0.48
rpoC 764355 p.Gln329Pro missense_variant 0.5
rpoC 764377 c.1008C>G synonymous_variant 0.59
rpoC 764380 c.1011G>C synonymous_variant 0.53
rpoC 764383 c.1014C>G synonymous_variant 0.53
rpoC 764387 c.1018_1020delTTGinsCTC synonymous_variant 0.56
rpoC 764398 c.1029G>C synonymous_variant 0.53
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.48
rpoC 764410 c.1041G>T synonymous_variant 0.5
rpoC 764428 c.1059G>T synonymous_variant 0.33
rpoC 764723 p.Phe452Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778430 p.Arg17Ser missense_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781406 c.-154_-153insC upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.17
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.38
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.54
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.65
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.64
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.58
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.54
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.54
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.57
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.53
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.5
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.5
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.17
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.42
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.46
rrs 1472574 n.729T>A non_coding_transcript_exon_variant 0.46
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.46
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.46
rrs 1472583 n.738T>A non_coding_transcript_exon_variant 0.43
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.5
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.5
rrs 1472599 n.754G>A non_coding_transcript_exon_variant 0.46
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.46
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.27
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.25
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.22
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.26
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.48
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.46
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.46
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.5
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.5
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.43
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.41
rrs 1473129 n.1286delG non_coding_transcript_exon_variant 0.22
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.53
rrs 1473149 n.1304G>C non_coding_transcript_exon_variant 0.64
rrs 1473162 n.1317C>G non_coding_transcript_exon_variant 0.68
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.65
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.67
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.62
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.63
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.66
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.61
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.61
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.61
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.13
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.31
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.36
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.36
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.43
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.43
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.25
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.14
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.14
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.14
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.68
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.76
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.76
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.76
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.77
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.8
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.81
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.79
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.84
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.84
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.8
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.74
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.72
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.67
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.66
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.61
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.52
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.36
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.22
rpsA 1833909 p.Asp123Ala missense_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834972 c.1431C>T synonymous_variant 0.93
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155600 p.Cys171Val missense_variant 0.5
katG 2155613 p.Phe167Leu missense_variant 0.5
katG 2155614 c.498T>C synonymous_variant 0.5
katG 2155617 p.Ile165Met missense_variant 0.64
katG 2155626 c.486G>C synonymous_variant 0.73
katG 2155637 p.Leu159Ile missense_variant 0.8
katG 2155641 p.Lys157Arg missense_variant 0.8
katG 2155650 c.462G>A synonymous_variant 0.82
katG 2155655 p.Lys153Gln missense_variant 0.82
katG 2155661 p.Val151Ile missense_variant 0.79
katG 2155668 c.444G>C synonymous_variant 0.86
katG 2155689 c.421_423delTTGinsCTC synonymous_variant 0.8
katG 2155704 c.408C>T synonymous_variant 0.86
katG 2155716 c.396T>C synonymous_variant 0.86
katG 2155722 c.390G>C synonymous_variant 0.84
katG 2155728 c.384G>C synonymous_variant 0.82
katG 2155735 p.Met126Gln missense_variant 0.77
katG 2155737 c.375C>T synonymous_variant 0.77
katG 2155741 p.Gly124Ala missense_variant 0.71
katG 2155743 c.369G>T synonymous_variant 0.71
katG 2155765 p.His116Thr missense_variant 0.5
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860346 p.Ser25Gly missense_variant 0.22
pepQ 2860349 p.Ile24Val missense_variant 0.2
thyA 3073979 p.Gln165* stop_gained 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613254 c.-138T>C upstream_gene_variant 0.17
alr 3840952 p.Lys157Glu missense_variant 1.0
embC 4240890 p.Trp343* stop_gained 0.13
embC 4241465 p.Phe535Leu missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
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