TB-Profiler result

Run: SRR11349189
Summary

Run ID: SRR11349189

Sample name:

Date: 02-04-2023 20:55:10

Number of reads: 4047298

Percentage reads mapped: 86.63

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 761139 p.His445Asp missense_variant 0.99 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.26 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288953 p.Gly97Cys missense_variant 1.0 pyrazinamide
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.12
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.15
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.14
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.13
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.15
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.17
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.17
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.22
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.2
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.18
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.22
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.19
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.18
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.2
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.2
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.23
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.17
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.16
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.17
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.15
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.2
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.26
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.14
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.26
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.21
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.21
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.14
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.21
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.16
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.11
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.11
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.12
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.12
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.13
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.16
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.12
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.12
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.14
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.14
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.14
rrl 1475978 n.2321C>T non_coding_transcript_exon_variant 0.1
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.14
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.11
rrl 1476001 n.2344T>C non_coding_transcript_exon_variant 0.11
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.1
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.12
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.15
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.14
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.14
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.15
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.14
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.15
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.21
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.15
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.14
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.27
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.38
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.48
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.56
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.6
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.55
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.55
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.47
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.53
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.51
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.38
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.2
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
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
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408048 p.Cys52Tyr missense_variant 1.0