TB-Profiler result

Run: SRR10315473
Summary

Run ID: SRR10315473

Sample name:

Date: 02-04-2023 17:06:47

Number of reads: 5808369

Percentage reads mapped: 88.68

Strain: lineage4.8.1

Drug-resistance: MDR-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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 1.0
lineage4.8.1 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
rpoB 761110 p.Asp435Val missense_variant 0.97 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288790 p.Leu151Ser missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326213 p.Arg421* stop_gained 0.17 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
mshA 576108 p.Ala254Gly missense_variant 0.25
rpoB 759691 c.-116A>T upstream_gene_variant 0.11
rpoB 760005 p.Ser67Pro missense_variant 0.11
rpoC 763384 p.Asn5Lys missense_variant 0.17
rpoC 763474 p.Asn35Lys missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776384 c.2097C>T synonymous_variant 0.12
mmpL5 776785 p.Glu566* stop_gained 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800664 c.-145G>T upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471975 n.130G>A non_coding_transcript_exon_variant 0.2
rrs 1472089 n.244C>T non_coding_transcript_exon_variant 0.27
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.25
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.23
rrs 1472108 n.263C>A non_coding_transcript_exon_variant 0.23
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.2
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.2
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.21
rrs 1472130 n.285G>A non_coding_transcript_exon_variant 0.21
rrs 1472135 n.290C>T non_coding_transcript_exon_variant 0.21
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.23
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.21
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.21
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.21
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.21
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.29
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.36
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.23
rrs 1472951 n.1106T>C non_coding_transcript_exon_variant 0.18
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.2
rrs 1472958 n.1113A>G non_coding_transcript_exon_variant 0.2
rrs 1472968 n.1123C>T non_coding_transcript_exon_variant 0.18
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.18
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.18
rrs 1472988 n.1143T>C non_coding_transcript_exon_variant 0.2
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.2
rrs 1473017 n.1172A>G non_coding_transcript_exon_variant 0.29
rrs 1473022 n.1177G>T non_coding_transcript_exon_variant 0.22
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.2
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.22
rrl 1473749 n.92A>T non_coding_transcript_exon_variant 0.25
rrl 1474169 n.512A>T non_coding_transcript_exon_variant 0.25
rrl 1474339 n.682C>A non_coding_transcript_exon_variant 0.29
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.22
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.12
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.11
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.11
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.12
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.12
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.18
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.12
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.22
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.17
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.19
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.39
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.17
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.29
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.24
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.19
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.4
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.27
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.13
rrl 1476404 n.2747G>A non_coding_transcript_exon_variant 0.24
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.24
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.28
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.33
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.33
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.19
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.19
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.12
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.25
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.13
rrl 1476474 n.2817C>T non_coding_transcript_exon_variant 0.14
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.46
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.25
rpsA 1834272 p.His244Leu missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102662 c.381C>G synonymous_variant 0.12
katG 2154150 c.1962C>A synonymous_variant 0.12
katG 2156015 p.Gly33Ser missense_variant 0.13
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2168521 p.Gln698Lys missense_variant 0.18
PPE35 2169431 c.1182G>A synonymous_variant 0.15
PPE35 2169943 p.Leu224Phe missense_variant 0.11
Rv1979c 2222118 c.1047G>T synonymous_variant 0.14
Rv1979c 2223143 p.Gly8* stop_gained 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3074138 p.Ile112Phe missense_variant 0.11
ald 3086756 c.-64A>T upstream_gene_variant 0.11
ald 3086876 c.57C>T synonymous_variant 0.17
fbiD 3339040 c.-78T>C upstream_gene_variant 1.0
whiB7 3568646 c.33delC frameshift_variant 0.11
fbiB 3642874 p.Leu447Arg missense_variant 1.0
clpC1 4038650 c.2055C>A synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267312 p.Gly509Trp missense_variant 0.13
ethR 4326565 c.-984C>A upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0