TB-Profiler result

Run: ERR4818509
Summary

Run ID: ERR4818509

Sample name:

Date: 01-04-2023 15:35:59

Number of reads: 2338112

Percentage reads mapped: 94.63

Strain: La1.2.BCG

Drug-resistance: RR-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
La1 M.bovis None None 1.0
La1.2 M.bovis None None 1.0
La1.2.BCG M.bovis BCG 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 761084 c.1280_1291delCCAGCCAGCTGA disruptive_inframe_deletion 1.0 rifampicin
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.3 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.38 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.36 kanamycin, capreomycin, aminoglycosides, amikacin
pncA 2289073 p.His57Asp 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
gyrB 5752 c.513G>A synonymous_variant 1.0
gyrA 6406 c.-896C>T upstream_gene_variant 1.0
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8285 c.984C>T synonymous_variant 1.0
gyrA 8624 c.1323G>T synonymous_variant 1.0
gyrA 8741 c.1440C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 761591 p.Asp595Glu missense_variant 0.97
rpoC 762917 c.-453C>T upstream_gene_variant 0.14
rpoC 762920 c.-450C>T upstream_gene_variant 0.15
rpoC 762929 c.-441G>T upstream_gene_variant 0.13
rpoC 762944 c.-426C>T upstream_gene_variant 0.14
rpoC 762956 c.-414G>T upstream_gene_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 0.97
rpoC 763572 p.Val68Ala missense_variant 1.0
rpoC 763575 p.Arg69Pro missense_variant 1.0
rpoC 765453 p.Ala695Val missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775765 p.Val906Ile missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781568 c.9C>T synonymous_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.25
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.31
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.31
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.4
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.82
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.84
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.66
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.5
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.4
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.5
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.69
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.64
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.59
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.59
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.29
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.5
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.29
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.58
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.55
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.5
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.92
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.38
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.44
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.44
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.42
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.29
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.33
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.22
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.29
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.42
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.41
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.41
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.4
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.39
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.51
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.37
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.49
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.38
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.35
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.5
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.15
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.27
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.45
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.73
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.84
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.8
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.82
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.82
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.85
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.8
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.79
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.8
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.82
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.83
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.83
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.8
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.79
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.75
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.75
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.71
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.71
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.73
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.73
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.71
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.76
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.76
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.72
rrs 1473204 n.1359C>T non_coding_transcript_exon_variant 0.38
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.44
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.43
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 0.33
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.25
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.25
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.6
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.8
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.8
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.8
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.83
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.83
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.8
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.67
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.67
rrl 1476253 n.2596A>G non_coding_transcript_exon_variant 0.67
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.67
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.67
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.67
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.57
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.81
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.86
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.83
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.83
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.67
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.54
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.43
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102106 p.Gly313Arg missense_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2156025 c.87C>A synonymous_variant 1.0
katG 2156465 c.-354C>T upstream_gene_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.98
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2168920 p.Val565Phe missense_variant 0.97
Rv1979c 2222308 p.Asp286Gly missense_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 1.0
Rv3083 3448745 p.Ile81Ser missense_variant 1.0
Rv3083 3448783 p.Val94Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4242029 c.2167C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247173 c.660G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269689 p.Val49Ile missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0