TB-Profiler result

Run: SRR1173040
Summary

Run ID: SRR1173040

Sample name:

Date: 03-04-2023 03:15:27

Number of reads: 1542376

Percentage reads mapped: 27.09

Strain: lineage4.4.1.1.1

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
lineage4.4 Euro-American S;T None 0.99
lineage4.4.1 Euro-American (S-type) S;T None 0.98
lineage4.4.1.1 Euro-American S;Orphans None 1.0
lineage4.4.1.1.1 Euro-American S;Orphans None 0.99
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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.83 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.97 isoniazid
pncA 2289142 p.Tyr34Asp missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val 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
gyrB 5152 c.-88C>A upstream_gene_variant 0.12
gyrB 5741 p.Gly168Trp missense_variant 0.17
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 576567 p.Arg407Leu missense_variant 0.12
ccsA 620240 p.Thr117Ile missense_variant 0.17
rpoB 761129 c.1323G>T synonymous_variant 0.18
rpoC 766314 p.Ser982Tyr missense_variant 0.15
rpoC 766487 p.Pro1040Ser missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775724 c.2757G>A synonymous_variant 0.13
mmpR5 778451 c.-539C>A upstream_gene_variant 0.17
mmpS5 778565 p.Cys114Tyr missense_variant 0.15
mmpL5 779238 c.-758G>T upstream_gene_variant 0.14
mmpR5 779323 p.Ala112Thr missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801276 c.468G>T synonymous_variant 0.15
rplC 801291 c.483C>T synonymous_variant 0.18
fbiC 1303001 p.Ser24* stop_gained 0.13
fbiC 1303162 p.Pro78Ser missense_variant 0.2
fbiC 1303843 p.Ala305Ser missense_variant 0.12
fbiC 1304679 p.Glu583Asp missense_variant 0.13
Rv1258c 1406872 p.Gly157Cys missense_variant 0.15
embR 1416704 p.Tyr215Cys missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.64
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.71
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.73
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.84
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.85
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.87
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.87
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.91
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.91
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.91
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.91
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.91
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.91
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.91
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.88
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.32
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.14
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.77
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.8
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.83
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.83
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.79
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.74
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.69
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.32
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.15
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.15
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.13
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.17
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.16
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.14
rrl 1474848 n.1191G>A non_coding_transcript_exon_variant 0.15
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.14
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.15
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.3
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.33
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.31
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.32
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.31
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.28
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.28
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.17
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.65
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.67
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.76
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.78
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.82
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.82
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.83
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.83
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.88
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.88
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.89
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.81
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.58
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.44
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.19
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918625 p.Pro229Gln missense_variant 0.2
ndh 2102037 p.Ala336Thr missense_variant 0.13
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2155012 p.Pro367Gln missense_variant 0.18
katG 2155422 c.690G>A synonymous_variant 0.13
katG 2155731 p.Gln127His missense_variant 0.15
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2170348 p.Gln89Lys missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289992 c.-751G>T upstream_gene_variant 0.14
pncA 2290079 c.-838T>C upstream_gene_variant 0.14
kasA 2518282 c.168A>G synonymous_variant 0.1
kasA 2518904 c.790C>A synonymous_variant 0.14
kasA 2518971 p.Arg286His missense_variant 0.15
ahpC 2725930 c.-263C>A upstream_gene_variant 0.14
ahpC 2725934 c.-259G>A upstream_gene_variant 0.14
folC 2746914 p.Asp229Asn missense_variant 0.13
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
ribD 2987503 p.Gly222Val missense_variant 0.2
Rv2752c 3064799 p.Arg465Trp missense_variant 0.14
Rv2752c 3064993 p.Trp400* stop_gained 1.0
Rv2752c 3066388 c.-197C>A upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339287 p.Arg57Leu missense_variant 1.0
fbiD 3339410 p.Ala98Asp missense_variant 0.15
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474666 c.660G>C synonymous_variant 0.15
fprA 3474697 p.Asp231Tyr missense_variant 0.13
fprA 3475325 p.Pro440His missense_variant 0.15
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
fbiA 3640856 p.Gly105Ala missense_variant 0.12
fbiB 3642132 p.Ala200Ser missense_variant 0.15
fbiB 3642616 p.Pro361His missense_variant 0.13
alr 3841195 p.Arg76Cys missense_variant 0.12
rpoA 3877791 c.717C>T synonymous_variant 0.13
panD 4044061 p.Ala74Asp missense_variant 0.14
embC 4240311 p.Pro150Gln missense_variant 0.14
embA 4242418 c.-815C>G upstream_gene_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245606 p.Leu792Met missense_variant 0.12
embB 4247018 p.Gly169Arg missense_variant 0.11
aftB 4268013 p.Pro275Arg missense_variant 0.12
ubiA 4269671 p.Val55Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407845 p.Glu120Gln missense_variant 0.17
gid 4407870 c.333C>A synonymous_variant 0.15