TB-Profiler result

Run: SRR1169145
Summary

Run ID: SRR1169145

Sample name:

Date: 03-04-2023 02:47:09

Number of reads: 608875

Percentage reads mapped: 68.27

Strain: lineage4.1.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 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
rpoB 761141 p.His445Gln missense_variant 1.0 rifampicin
rpoB 761161 p.Leu452Pro missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288953 p.Gly97Cys missense_variant 1.0 pyrazinamide
embB 4248003 p.Gln497Arg 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
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406999 c.342C>A synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.16
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.15
rrs 1472129 n.284G>A non_coding_transcript_exon_variant 0.15
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.16
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.14
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.15
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.18
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.16
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.11
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.1
rrs 1472708 n.863T>A non_coding_transcript_exon_variant 0.15
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.28
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.28
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.26
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.28
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.29
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.22
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.14
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.14
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.13
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.12
rrs 1473262 n.1417T>A non_coding_transcript_exon_variant 0.13
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.16
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.23
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.23
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.23
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.23
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.28
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.25
rrl 1475869 n.2212C>T non_coding_transcript_exon_variant 0.24
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.26
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.27
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.32
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.32
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.31
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.31
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.31
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.31
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.33
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.38
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.38
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.38
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.46
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.47
rrl 1476353 n.2696G>A non_coding_transcript_exon_variant 0.32
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.3
rrl 1476359 n.2702C>T non_coding_transcript_exon_variant 0.28
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.4
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.4
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.51
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.51
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.54
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.49
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.46
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.44
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.43
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.39
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.21
rrl 1476513 n.2856G>A non_coding_transcript_exon_variant 0.12
rrl 1476577 n.2920T>A non_coding_transcript_exon_variant 0.11
rrl 1476578 n.2921C>A non_coding_transcript_exon_variant 0.11
rrl 1476592 n.2935G>A non_coding_transcript_exon_variant 0.1
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.1
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.1
rrl 1476605 n.2948C>T non_coding_transcript_exon_variant 0.1
rpsA 1833427 c.-115G>A upstream_gene_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726210 c.18T>C synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641447 p.Thr302Met missense_variant 1.0
rpoA 3877553 p.Glu319Lys missense_variant 1.0
rpoA 3878601 c.-95delG upstream_gene_variant 0.27
embC 4240897 c.1035C>G synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
ubiA 4269731 p.Ala35Thr missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407756 p.Ser149Arg missense_variant 1.0