TB-Profiler result

Run: SRR1048869
Summary

Run ID: SRR1048869

Sample name:

Date: 02-04-2023 17:49:14

Number of reads: 400108

Percentage reads mapped: 11.19

Strain: lineage2.2.2

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 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 0.08
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.Asp94Gly missense_variant 0.69 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.56 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.8 streptomycin
inhA 1674048 c.-154G>A upstream_gene_variant 0.5 isoniazid, ethionamide
katG 2155693 p.Ser140Asn missense_variant 0.67 isoniazid
katG 2155732 p.Gln127Pro missense_variant 0.41 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 0.8 pyrazinamide
folC 2747151 p.Ser150Gly missense_variant 0.6 para-aminosalicylic_acid
embB 4247429 p.Met306Leu missense_variant 0.58 ethambutol
embB 4247730 p.Gly406Asp missense_variant 0.5 ethambutol
ethA 4326459 c.1004_1014delCTGACATCATC frameshift_variant 0.64 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 575907 p.Ala187Val missense_variant 0.78
ccsA 620625 p.Ile245Met missense_variant 0.64
rpoC 762893 c.-477C>T upstream_gene_variant 0.6
rpoC 762896 c.-474G>C upstream_gene_variant 0.67
rpoC 762917 c.-453C>G upstream_gene_variant 0.76
rpoC 762920 c.-450C>T upstream_gene_variant 0.76
rpoC 762923 c.-447C>G upstream_gene_variant 0.73
rpoB 762925 p.Thr1040Ile missense_variant 0.73
rpoC 762929 c.-441G>T upstream_gene_variant 0.7
rpoB 762939 p.Met1045Leu missense_variant 0.67
rpoB 762942 p.Ile1046Val missense_variant 0.67
rpoC 762965 c.-405T>C upstream_gene_variant 0.64
rpoC 762980 c.-390T>C upstream_gene_variant 0.68
rpoC 762989 c.-381G>C upstream_gene_variant 0.56
rpoC 762995 c.-375G>C upstream_gene_variant 0.42
rpoC 762998 c.-372G>A upstream_gene_variant 0.36
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764329 c.960C>T synonymous_variant 0.38
rpoC 764338 p.Glu323Asp missense_variant 0.47
rpoC 764344 c.975C>T synonymous_variant 0.53
rpoC 764348 p.Met327Leu missense_variant 0.53
rpoC 764355 p.Gln329Pro missense_variant 0.6
rpoC 764377 c.1008C>G synonymous_variant 0.59
rpoC 764380 c.1011G>C synonymous_variant 0.57
rpoC 764383 c.1014C>G synonymous_variant 0.57
rpoC 764387 c.1018_1020delTTGinsCTC synonymous_variant 0.59
rpoC 764398 c.1029G>C synonymous_variant 0.59
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.57
rpoC 764410 c.1041G>T synonymous_variant 0.54
rpoC 764428 c.1059G>T synonymous_variant 0.38
rpoC 764434 c.1065A>G synonymous_variant 0.28
rpoC 764435 c.1066A>C synonymous_variant 0.28
rpoC 764443 p.Ile358Met missense_variant 0.23
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406945 c.396C>T synonymous_variant 0.4
embR 1416229 c.1119C>T synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.38
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.45
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.63
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.76
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.73
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.76
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.76
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.75
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.75
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.72
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.69
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.69
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.56
rrs 1472694 n.849C>G non_coding_transcript_exon_variant 0.2
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.27
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.45
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.45
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.45
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.5
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.65
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.65
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.62
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.61
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.52
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.47
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.42
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.44
rrs 1473149 n.1304G>C non_coding_transcript_exon_variant 0.53
rrs 1473162 n.1317C>G non_coding_transcript_exon_variant 0.53
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.56
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.56
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.56
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.69
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.69
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.64
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.64
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.64
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 0.71
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.2
rrl 1474801 n.1145delT non_coding_transcript_exon_variant 0.17
rrl 1474825 n.1168G>A non_coding_transcript_exon_variant 0.25
rrl 1474828 n.1171G>C non_coding_transcript_exon_variant 0.25
rrl 1474832 n.1176delG non_coding_transcript_exon_variant 0.25
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.33
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.33
rrl 1474875 n.1218G>A non_coding_transcript_exon_variant 0.33
rrl 1474876 n.1219T>A non_coding_transcript_exon_variant 0.29
rrl 1474883 n.1226T>C non_coding_transcript_exon_variant 0.29
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.29
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.25
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.25
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.5
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.5
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.45
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.45
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.4
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.4
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.33
rrl 1475894 n.2237C>A non_coding_transcript_exon_variant 0.33
rrl 1475904 n.2247G>A non_coding_transcript_exon_variant 0.2
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.2
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.44
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.59
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.59
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.59
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.56
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.76
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.76
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.78
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.86
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.86
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.86
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.8
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.77
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.7
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.7
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.67
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.7
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.4
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.22
rpsA 1833594 p.Ser18Tyr missense_variant 0.57
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155413 c.699G>A synonymous_variant 0.14
katG 2155600 p.Cys171Val missense_variant 0.67
katG 2155613 p.Phe167Leu missense_variant 0.64
katG 2155614 c.498T>C synonymous_variant 0.6
katG 2155617 p.Ile165Met missense_variant 0.6
katG 2155626 c.486G>C synonymous_variant 0.65
katG 2155637 p.Leu159Ile missense_variant 0.58
katG 2155641 p.Lys157Arg missense_variant 0.61
katG 2155650 c.462G>A synonymous_variant 0.61
katG 2155655 p.Lys153Gln missense_variant 0.61
katG 2155661 p.Val151Ile missense_variant 0.61
katG 2155668 c.444G>C synonymous_variant 0.61
katG 2155689 c.421_423delTTGinsCTC synonymous_variant 0.62
katG 2155704 c.408C>T synonymous_variant 0.67
katG 2155716 c.396T>C synonymous_variant 0.62
katG 2155722 c.390G>C synonymous_variant 0.5
katG 2155728 c.384G>C synonymous_variant 0.41
katG 2155735 p.Met126Gln missense_variant 0.41
katG 2155737 c.375C>T synonymous_variant 0.44
katG 2155741 p.Gly124Ala missense_variant 0.47
katG 2155743 c.369G>T synonymous_variant 0.44
katG 2155765 p.His116Thr missense_variant 0.44
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170256 c.357G>T synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518800 p.Pro229Gln missense_variant 0.29
ahpC 2726146 c.-47_-46insT upstream_gene_variant 0.71
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448958 p.Asp152Ala missense_variant 0.62
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474765 c.759T>C synonymous_variant 0.64
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3841405 p.Glu6Gln missense_variant 0.75
rpoA 3877960 p.Val183Gly missense_variant 0.7
clpC1 4039526 c.1179G>T synonymous_variant 0.17
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