TB-Profiler result

Run: SRR11342667
Summary

Run ID: SRR11342667

Sample name:

Date: 02-04-2023 20:47:39

Number of reads: 2283215

Percentage reads mapped: 28.89

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
ethA 4327484 c.-11A>G upstream_gene_variant 1.0 ethionamide
pncA 2288565 c.377_*115del frameshift_variant&stop_lost&splice_region_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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.28
mshA 576113 p.Arg256Gly missense_variant 0.19
rpoC 762899 c.-471G>C upstream_gene_variant 0.16
rpoC 762923 c.-447C>G upstream_gene_variant 0.17
rpoB 762925 p.Thr1040Ile missense_variant 0.17
rpoB 762934 c.3129_3130insAGCC frameshift_variant 0.15
rpoB 762938 c.3133_3136delATGA frameshift_variant 0.14
rpoC 762965 c.-405T>C upstream_gene_variant 0.17
rpoC 764560 c.1191T>G synonymous_variant 0.16
rpoC 764575 c.1206T>G synonymous_variant 0.58
rpoC 764581 c.1212T>C synonymous_variant 0.62
rpoC 764582 p.Leu405Met missense_variant 0.63
rpoC 764587 c.1218C>G synonymous_variant 0.66
rpoC 764605 c.1236G>C synonymous_variant 0.63
rpoC 764611 c.1242G>C synonymous_variant 0.63
rpoC 764632 c.1263T>C synonymous_variant 0.62
rpoC 764641 c.1272C>T synonymous_variant 0.6
rpoC 764650 c.1281G>T synonymous_variant 0.57
rpoC 764663 p.Val432Thr missense_variant 0.52
rpoC 764668 c.1299C>G synonymous_variant 0.54
rpoC 764672 p.Gln435Glu missense_variant 0.55
rpoC 764677 c.1308C>G synonymous_variant 0.52
rpoC 764695 c.1326T>C synonymous_variant 0.49
rpoC 764701 c.1332C>G synonymous_variant 0.42
rpoC 764705 p.Leu446Lys missense_variant 0.41
rpoC 764716 c.1347G>C synonymous_variant 0.35
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765619 p.Glu750Asp 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 1472120 n.275G>C non_coding_transcript_exon_variant 0.12
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.12
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.12
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.12
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.12
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.14
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.12
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.14
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.3
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.4
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.38
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.37
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.37
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.37
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.36
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.36
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.35
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.32
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.25
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.13
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.16
rrs 1472379 n.534T>A non_coding_transcript_exon_variant 0.16
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 0.15
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.21
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 0.2
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.21
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.38
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.39
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.4
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.33
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.31
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.29
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.25
rrs 1472826 n.981G>C non_coding_transcript_exon_variant 0.21
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.15
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.17
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.18
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 1475881 n.2224T>C non_coding_transcript_exon_variant 0.12
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.12
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.11
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 1.0
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.1
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.11
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.11
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.24
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.24
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.27
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.64
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.74
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.73
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.76
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.75
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.79
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.81
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.78
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.79
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.78
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.74
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.73
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.68
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.67
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.62
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.61
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.5
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.4
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.37
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.26
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.21
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.23
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223051 p.Glu38Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
pepQ 2860342 p.Asp26Ala missense_variant 1.0
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074160 c.312A>G synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878618 c.-111A>C upstream_gene_variant 0.33
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4407912 c.160_290del frameshift_variant 1.0