TB-Profiler result

Run: SRR16149129
Summary

Run ID: SRR16149129

Sample name:

Date: 03-04-2023 16:28:50

Number of reads: 2812051

Percentage reads mapped: 71.82

Strain: lineage4.2.2.1

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
lineage4.2 Euro-American H;T;LAM None 0.99
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.99
lineage4.2.2.1 Euro-American LAM7-TUR 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 761139 p.His445Asp missense_variant 0.99 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674782 p.Ile194Thr missense_variant 1.0 isoniazid, 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
mshA 576077 c.730C>T synonymous_variant 1.0
rpoB 762053 c.2247T>C synonymous_variant 0.13
rpoB 762057 p.Ile751Val missense_variant 0.1
rpoB 762062 c.2256T>C synonymous_variant 0.1
rpoB 762065 c.2259T>C synonymous_variant 0.13
rpoB 762101 c.2295C>G synonymous_variant 0.1
rpoB 762114 p.Ile770Val missense_variant 0.13
rpoB 762233 c.2427G>C synonymous_variant 0.15
rpoB 762254 c.2448T>C synonymous_variant 0.12
rpoB 762293 c.2487T>G synonymous_variant 0.12
rpoB 762299 c.2493G>C synonymous_variant 0.14
rpoC 763528 c.159G>C synonymous_variant 0.11
rpoC 763534 c.165T>C synonymous_variant 0.14
rpoC 763546 c.177A>G synonymous_variant 0.18
rpoC 763555 c.186C>T synonymous_variant 0.14
rpoC 763573 c.204G>C synonymous_variant 0.15
rpoC 763594 c.225C>T synonymous_variant 0.17
rpoC 763615 c.246G>C synonymous_variant 0.13
rpoC 764405 c.1036A>C synonymous_variant 0.11
rpoC 764435 c.1066A>C synonymous_variant 0.11
rpoC 764461 c.1092A>G synonymous_variant 0.12
rpoC 764503 c.1134G>C synonymous_variant 0.11
rpoC 764521 c.1152T>C synonymous_variant 0.16
rpoC 764539 c.1170C>G synonymous_variant 0.13
rpoC 764560 c.1191T>C synonymous_variant 0.11
rpoC 764566 c.1197C>G synonymous_variant 0.13
rpoC 764575 c.1206T>G synonymous_variant 0.13
rpoC 764581 c.1212T>C synonymous_variant 0.14
rpoC 764582 p.Leu405Met missense_variant 0.14
rpoC 764611 c.1242G>C synonymous_variant 0.15
rpoC 764632 c.1263T>C synonymous_variant 0.19
rpoC 764650 c.1281G>T synonymous_variant 0.12
rpoC 764662 c.1293G>C synonymous_variant 0.14
rpoC 764695 c.1326T>C synonymous_variant 0.12
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 1472150 n.305T>A non_coding_transcript_exon_variant 0.22
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.2
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.15
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.12
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.12
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.14
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.15
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.17
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.15
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.16
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.16
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.15
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.17
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.17
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.12
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.17
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.12
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.14
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.14
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.21
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.19
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.12
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.17
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.12
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.11
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.1
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.12
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.11
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.12
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.12
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.14
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.12
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.12
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.16
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.13
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.11
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.14
rpsA 1833970 c.429G>C synonymous_variant 0.13
rpsA 1833979 c.438T>C synonymous_variant 0.14
rpsA 1834012 c.471G>C synonymous_variant 0.15
rpsA 1834015 c.474G>C synonymous_variant 0.12
rpsA 1834069 c.528G>C synonymous_variant 0.15
rpsA 1834261 c.720A>G synonymous_variant 0.13
rpsA 1834264 c.723G>C synonymous_variant 0.12
rpsA 1834306 c.765T>C synonymous_variant 0.11
rpsA 1834451 c.910T>C synonymous_variant 0.14
rpsA 1834468 c.927A>G synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102726 p.His106Arg missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3877848 c.660C>T synonymous_variant 0.12
rpoA 3877893 c.615C>G synonymous_variant 0.11
rpoA 3877962 c.546G>C synonymous_variant 0.12
rpoA 3877971 p.Asp179Glu missense_variant 0.11
clpC1 4039838 p.Leu289Ile missense_variant 0.11
clpC1 4039850 c.855T>C synonymous_variant 0.12
clpC1 4039865 c.840T>C synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408009 p.Val65Ala missense_variant 1.0