TB-Profiler result

Run: SRR18002873
Summary

Run ID: SRR18002873

Sample name:

Date: 03-04-2023 19:07:18

Number of reads: 1459589

Percentage reads mapped: 34.95

Strain: lineage4.4.2;lineage4.2.2;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 0.49
lineage4.2 Euro-American H;T;LAM None 0.28
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.48
lineage4.4 Euro-American S;T None 0.14
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.3
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.46
lineage4.4.2 Euro-American T1;T2 None 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 7570 p.Ala90Val missense_variant 0.14 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7572 p.Ser91Pro missense_variant 0.74 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 0.17 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Tyr missense_variant 0.36 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.39 rifampicin
rpoB 761185 p.Glu460Gly missense_variant 0.32 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.62 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.24 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.2 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.69 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 0.75 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.52 ethambutol
embB 4247574 p.Asp354Ala missense_variant 0.11 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 0.51
mshA 575907 p.Ala187Val missense_variant 0.29
mshA 576077 c.730C>T synonymous_variant 0.43
mshA 576108 p.Ala254Gly missense_variant 0.22
mshA 576588 p.Gly414Val missense_variant 0.21
ccsA 620625 p.Ile245Met missense_variant 0.61
rpoB 761036 c.1230G>C synonymous_variant 0.11
rpoB 761037 c.1231T>C synonymous_variant 0.11
rpoB 761046 p.Ile414Val missense_variant 0.11
rpoB 761051 c.1245G>C synonymous_variant 0.12
rpoB 761057 c.1251G>C synonymous_variant 0.12
rpoC 762980 c.-390T>C upstream_gene_variant 0.15
rpoC 762989 c.-381G>C upstream_gene_variant 0.17
rpoC 762995 c.-375G>C upstream_gene_variant 0.18
rpoC 762998 c.-372G>A upstream_gene_variant 0.2
rpoB 763005 p.Cys1067Val missense_variant 0.21
rpoC 763013 c.-357C>G upstream_gene_variant 0.19
rpoB 763014 p.Met1070Leu missense_variant 0.2
rpoC 763022 c.-348C>G upstream_gene_variant 0.18
rpoC 763025 c.-345C>T upstream_gene_variant 0.18
rpoC 763028 c.-342T>C upstream_gene_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 0.61
rpoC 763628 p.Val87Met missense_variant 0.15
rpoC 764581 c.1212T>C synonymous_variant 0.11
rpoC 764605 c.1236G>C synonymous_variant 0.11
rpoC 764632 c.1263T>C synonymous_variant 0.18
rpoC 764641 c.1272C>T synonymous_variant 0.12
rpoC 764650 c.1281G>T synonymous_variant 0.2
rpoC 764663 p.Val432Thr missense_variant 0.12
rpoC 764672 p.Gln435Glu missense_variant 0.13
rpoC 764695 c.1326T>C synonymous_variant 0.15
rpoC 764706 p.Leu446Gln missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.59
mmpL5 776182 p.Asp767Asn missense_variant 0.58
mmpS5 779615 c.-710C>G upstream_gene_variant 0.56
rpsL 781395 c.-165T>C upstream_gene_variant 0.97
Rv1258c 1406760 c.580_581insC frameshift_variant 0.62
embR 1417227 p.Met41Val missense_variant 0.34
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.21
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.14
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.19
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.15
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.14
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.12
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.11
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.15
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.12
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.13
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.13
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.13
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.14
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.13
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.13
rrs 1472826 n.981G>C non_coding_transcript_exon_variant 0.13
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.14
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.14
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.11
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.14
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.11
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.11
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.16
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.13
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.13
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.12
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.18
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.18
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.18
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.18
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.24
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.21
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.18
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.15
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 0.14
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.14
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.12
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.13
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.17
rrl 1474275 n.618T>G non_coding_transcript_exon_variant 0.11
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.11
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.15
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.14
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.11
rrl 1474932 n.1275C>T non_coding_transcript_exon_variant 0.12
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.17
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.18
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.15
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.2
rrl 1476266 n.2609G>A non_coding_transcript_exon_variant 0.16
rrl 1476279 n.2622G>T non_coding_transcript_exon_variant 0.17
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.17
rrl 1476281 n.2624T>A non_coding_transcript_exon_variant 0.18
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.16
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.19
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.16
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.16
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.17
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.17
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.2
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.22
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.21
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.4
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.44
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.48
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.47
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.48
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.49
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.52
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.53
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.49
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.47
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.44
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.44
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.42
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.44
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.41
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.4
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.23
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.19
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.29
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.11
inhA 1673829 c.-373C>T upstream_gene_variant 0.37
rpsA 1834177 c.636A>C synonymous_variant 0.62
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.55
PPE35 2167926 p.Leu896Ser missense_variant 0.38
PPE35 2168471 p.Phe714Leu missense_variant 0.19
PPE35 2170048 p.Leu189Val missense_variant 0.13
PPE35 2170053 p.Thr187Ser missense_variant 0.14
PPE35 2170802 c.-190T>C upstream_gene_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726381 c.189C>A synonymous_variant 0.36
ahpC 2726746 p.Leu185Arg missense_variant 0.11
Rv2752c 3066099 p.Met31Ile missense_variant 0.27
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.24
ald 3086742 c.-78A>C upstream_gene_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087536 c.717C>A synonymous_variant 0.11
Rv3083 3448948 p.Tyr149Asp missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474858 c.852G>C synonymous_variant 0.14
Rv3236c 3612469 c.648A>G synonymous_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 0.38
alr 3841567 c.-147A>G upstream_gene_variant 0.38
clpC1 4040021 c.684A>C synonymous_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.35
embB 4246508 c.-6G>A upstream_gene_variant 0.31
embB 4246544 p.Thr11Pro missense_variant 0.13
embB 4246548 p.Pro12Gln missense_variant 0.13
embB 4246556 p.Ala15Pro missense_variant 0.11
embB 4246563 p.Leu17Trp missense_variant 0.1
aftB 4267647 p.Asp397Gly missense_variant 0.58
aftB 4269375 c.-539G>A upstream_gene_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.55
gid 4407927 p.Glu92Asp missense_variant 0.67
gid 4408103 p.Gly34Arg missense_variant 0.11