TB-Profiler result

Run: SRR1013566
Summary

Run ID: SRR1013566

Sample name:

Date: 02-04-2023 15:55:05

Number of reads: 1519712

Percentage reads mapped: 38.17

Strain: lineage4.4.2

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.4 Euro-American S;T None 1.0
lineage4.4.2 Euro-American T1;T2 None 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
gyrB 6749 p.Ala504Thr missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155693 p.Ser140Asn missense_variant 0.19 isoniazid
ahpC 2726145 c.-48G>A upstream_gene_variant 1.0 isoniazid
embB 4247730 p.Gly406Ala 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
mshA 576318 c.971_972insA frameshift_variant 0.2
rpoB 759939 p.Pro45Ala missense_variant 1.0
rpoC 762893 c.-477C>T upstream_gene_variant 0.14
rpoC 762896 c.-474G>C upstream_gene_variant 0.14
rpoC 762917 c.-453C>G upstream_gene_variant 0.18
rpoC 762920 c.-450C>T upstream_gene_variant 0.18
rpoC 762923 c.-447C>G upstream_gene_variant 0.18
rpoB 762925 p.Thr1040Ile missense_variant 0.18
rpoC 762929 c.-441G>T upstream_gene_variant 0.17
rpoB 762939 p.Met1045Leu missense_variant 0.18
rpoB 762942 p.Ile1046Val missense_variant 0.18
rpoC 762965 c.-405T>C upstream_gene_variant 0.19
rpoC 762980 c.-390T>C upstream_gene_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471832 n.-14A>G upstream_gene_variant 1.0
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.1
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.13
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.21
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.26
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.23
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.22
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.22
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.15
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.15
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.13
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.19
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.19
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.2
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.19
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.16
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.16
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.16
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.13
rrs 1473149 n.1304G>C non_coding_transcript_exon_variant 0.12
rrs 1473162 n.1317C>G non_coding_transcript_exon_variant 0.15
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.14
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.12
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.12
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.12
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.12
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.12
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.11
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.11
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.15
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.14
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.14
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.14
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.15
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.22
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.24
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.25
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.33
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.33
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.42
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.36
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.35
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.33
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.29
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.3
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.3
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.19
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.15
rpsA 1833692 p.Val51Leu missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918333 p.Glu132Ser missense_variant 0.13
katG 2154134 p.Asn660Asp missense_variant 1.0
katG 2155601 p.Cys171Gly missense_variant 0.12
katG 2155626 c.486G>C synonymous_variant 0.15
katG 2155668 c.444G>C synonymous_variant 0.17
katG 2155689 c.421_423delTTGinsCTC synonymous_variant 0.19
katG 2155704 c.408C>T synonymous_variant 0.21
katG 2155716 c.396T>C synonymous_variant 0.22
katG 2155722 c.390G>C synonymous_variant 0.18
katG 2155728 c.384G>C synonymous_variant 0.21
katG 2155735 p.Met126Gln missense_variant 0.24
katG 2155737 c.375C>T synonymous_variant 0.24
katG 2155741 p.Gly124Ala missense_variant 0.29
katG 2155743 c.369G>T synonymous_variant 0.29
katG 2155765 p.His116Pro missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288944 p.Thr100Pro missense_variant 1.0
pepQ 2860227 c.192C>G synonymous_variant 0.94
Rv2752c 3066099 p.Met31Ile missense_variant 1.0
thyX 3067949 c.-4C>T upstream_gene_variant 1.0
thyA 3074057 p.Glu139* stop_gained 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087350 c.531C>G synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841392 p.Lys10Met missense_variant 1.0
rpoA 3878157 c.351C>G synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246508 c.-6G>A upstream_gene_variant 1.0
aftB 4267262 c.1575T>C synonymous_variant 1.0
aftB 4268032 p.Pro269Ala missense_variant 0.12
aftB 4268928 c.-92C>T upstream_gene_variant 0.98
ubiA 4269296 p.Met180Val missense_variant 1.0
aftB 4269375 c.-539G>A upstream_gene_variant 1.0
ethA 4326860 p.Leu205Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408103 p.Gly34Trp missense_variant 0.88
ald 3087182 c.364_532del frameshift_variant 1.0