TB-Profiler result

Run: SRR4034391

Summary

Run ID: SRR4034391

Sample name:

Date: 04-04-2023 06:46:39

Number of reads: 13923902

Percentage reads mapped: 57.05

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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.His445Tyr missense_variant 0.99 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289031 p.His71Tyr missense_variant 0.99 pyrazinamide
ald 3086951 c.133delA frameshift_variant 1.0 cycloserine
embA 4243217 c.-16C>G upstream_gene_variant 1.0 ethambutol
embB 4247728 p.Glu405Asp missense_variant 0.99 ethambutol
gid 4407802 p.Ala134Glu missense_variant 1.0 streptomycin
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
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 762863 c.-507T>G upstream_gene_variant 0.11
rpoB 762872 p.Met1022Ile missense_variant 0.2
rpoB 762878 p.Ile1024Met missense_variant 0.22
rpoB 762879 p.Met1025Leu missense_variant 0.23
rpoC 762899 c.-471G>C upstream_gene_variant 0.33
rpoB 762925 p.Thr1040Ile missense_variant 0.38
rpoC 762929 c.-441G>C upstream_gene_variant 0.37
rpoB 762939 p.Met1045Leu missense_variant 0.33
rpoB 762942 p.Ile1046Val missense_variant 0.31
rpoC 762980 c.-390T>C upstream_gene_variant 0.18
rpoC 762983 c.-387C>T upstream_gene_variant 0.17
rpoC 762989 c.-381G>C upstream_gene_variant 0.16
rpoC 762998 c.-372G>A upstream_gene_variant 0.14
rpoC 764419 c.1050C>G synonymous_variant 0.12
rpoC 764428 c.1059G>C synonymous_variant 0.12
rpoC 764434 c.1065A>G synonymous_variant 0.11
rpoC 764435 c.1066_1068delAGGinsCGC synonymous_variant 0.12
rpoC 764443 p.Ile358Met missense_variant 0.11
rpoC 764446 p.Asp359Glu missense_variant 0.11
rpoC 764450 p.Gly361Arg missense_variant 0.11
rpoC 764461 p.Glu364Asp missense_variant 0.12
rpoC 764471 p.Asn368Arg missense_variant 0.11
rpoC 764479 c.1110G>A synonymous_variant 0.12
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 1406813 c.528T>C synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471876 n.31G>A non_coding_transcript_exon_variant 0.21
rrs 1471877 n.32A>G non_coding_transcript_exon_variant 0.21
rrs 1471892 n.47G>A non_coding_transcript_exon_variant 0.21
rrs 1471893 n.48T>G non_coding_transcript_exon_variant 0.22
rrs 1471896 n.51T>C non_coding_transcript_exon_variant 0.22
rrs 1471917 n.72G>A non_coding_transcript_exon_variant 0.26
rrs 1471918 n.74_78delAAGGT non_coding_transcript_exon_variant 0.27
rrs 1471934 n.89A>T non_coding_transcript_exon_variant 0.26
rrs 1471935 n.92_96delCTCGA non_coding_transcript_exon_variant 0.28
rrs 1471948 n.103A>G non_coding_transcript_exon_variant 0.27
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.17
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.19
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.21
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.2
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.22
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.19
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.12
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.11
rrs 1472338 n.493A>C non_coding_transcript_exon_variant 0.14
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.15
rrs 1472349 n.504A>T non_coding_transcript_exon_variant 0.16
rrs 1472374 n.529T>A non_coding_transcript_exon_variant 0.16
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.16
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 0.16
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.13
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.51
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 0.5
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.5
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.66
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.66
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.66
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.66
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.64
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.56
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.47
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.12
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.14
rrl 1474838 n.1181C>T non_coding_transcript_exon_variant 0.23
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.25
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.25
rrl 1474875 n.1218G>A non_coding_transcript_exon_variant 0.28
rrl 1474876 n.1219T>A non_coding_transcript_exon_variant 0.28
rrl 1474883 n.1226T>C non_coding_transcript_exon_variant 0.27
rrl 1474893 n.1236G>A non_coding_transcript_exon_variant 0.27
rrl 1474899 n.1242T>C non_coding_transcript_exon_variant 0.27
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 0.26
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.26
rrl 1474910 n.1253C>G non_coding_transcript_exon_variant 0.28
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.27
rrl 1474920 n.1263G>A non_coding_transcript_exon_variant 0.27
rrl 1475499 n.1842C>G non_coding_transcript_exon_variant 0.15
rrl 1475539 n.1882A>T non_coding_transcript_exon_variant 0.16
rrl 1475540 n.1883C>T non_coding_transcript_exon_variant 0.17
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.16
rrl 1475550 n.1893A>G non_coding_transcript_exon_variant 0.15
rrl 1475553 n.1896G>C non_coding_transcript_exon_variant 0.14
rrl 1475555 n.1898T>G non_coding_transcript_exon_variant 0.15
rrl 1475571 n.1914A>T non_coding_transcript_exon_variant 0.15
rrl 1475575 n.1918C>A non_coding_transcript_exon_variant 0.14
rrl 1475577 n.1920C>G non_coding_transcript_exon_variant 0.14
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.23
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.31
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.31
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.35
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.36
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.22
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.22
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.25
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.27
rrl 1476266 n.2609G>A non_coding_transcript_exon_variant 0.28
rrl 1476279 n.2622G>C non_coding_transcript_exon_variant 0.3
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.3
rrl 1476281 n.2624T>A non_coding_transcript_exon_variant 0.3
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.32
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.32
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.32
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.32
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.5
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.51
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.52
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.72
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.72
rrl 1476339 n.2682G>A non_coding_transcript_exon_variant 0.74
rrl 1476356 n.2699C>T non_coding_transcript_exon_variant 0.78
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.77
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.75
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.75
rrl 1476384 n.2727G>A non_coding_transcript_exon_variant 0.75
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.78
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.79
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.7
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.69
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.62
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.61
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.6
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.59
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.59
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.6
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.43
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.38
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T 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
alr 3840259 p.Tyr388Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4247738 p.Ala409Pro missense_variant 0.99
ethA 4326842 p.Tyr211Ser missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0