TB-Profiler result

Run: ERR4821413
Summary

Run ID: ERR4821413

Sample name:

Date: 01-04-2023 17:14:28

Number of reads: 323435

Percentage reads mapped: 88.21

Strain: La3

Drug-resistance: Other

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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
La3 M.orygis None 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.96 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
gyrB 5495 p.Val86Phe missense_variant 0.29
gyrB 5516 p.Ile93Val missense_variant 1.0
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrB 6717 p.Ile493Thr missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7775 c.474C>T synonymous_variant 1.0
gyrA 8930 c.1629C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490661 c.-122_-121insGCGAGC upstream_gene_variant 0.83
fgd1 490932 p.His50Gln missense_variant 0.33
fgd1 491453 p.Gly224Val missense_variant 0.33
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491749 p.Leu323Phe missense_variant 1.0
mshA 575347 c.-1G>A upstream_gene_variant 0.14
mshA 576108 p.Ala254Gly missense_variant 0.38
rpoB 762042 p.Ile746Val missense_variant 0.5
rpoB 762352 c.2557_2562dupGACGAG conservative_inframe_insertion 0.83
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764420 p.Asn351Asp missense_variant 0.22
rpoC 765659 p.Ala764Thr missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776726 c.1755C>T synonymous_variant 0.2
mmpL5 776732 c.1749C>T synonymous_variant 0.18
mmpL5 776735 c.1746C>T synonymous_variant 0.2
mmpL5 776738 c.1743C>T synonymous_variant 0.18
mmpL5 776741 c.1740C>G synonymous_variant 0.2
mmpL5 776744 c.1735_1737delCGCinsAGG synonymous_variant 0.22
mmpL5 778093 p.Trp130Gly missense_variant 0.38
mmpL5 778275 p.Ala69Val missense_variant 0.67
mmpS5 778641 p.Ser89Pro missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781878 p.Val107Ile missense_variant 0.29
rplC 800701 c.-108G>A upstream_gene_variant 0.22
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1305055 p.Met709Val missense_variant 0.33
fbiC 1305101 p.Asn724Ser missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 1.0
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 1.0
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 1.0
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 1.0
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 1.0
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 1.0
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 1.0
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 1.0
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 1.0
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 1.0
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 1.0
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 1.0
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 1.0
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 1.0
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 1.0
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 1.0
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.93
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.9
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.9
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.86
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.83
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.5
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.4
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.4
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.5
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.5
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.5
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.6
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.6
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.6
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.6
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.6
rrl 1473610 n.-48C>A upstream_gene_variant 0.4
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.67
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.67
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.4
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.8
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.4
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.8
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.67
inhA 1673680 c.-522C>G upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154134 p.Asn660Asp missense_variant 0.25
katG 2154567 c.1545C>T synonymous_variant 0.29
katG 2154707 p.Val469Leu missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155503 c.609C>T synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169279 c.1312_1333delAACAATGGTGTCTTTTACCGTG frameshift_variant 1.0
PPE35 2169615 p.Asn333Ser missense_variant 0.33
PPE35 2170669 c.-57G>A upstream_gene_variant 1.0
Rv1979c 2221789 p.Val459Ala missense_variant 0.18
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223130 p.His12Leu missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289978 c.-737T>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726378 c.186T>A synonymous_variant 1.0
ahpC 2726487 p.Gln99Glu missense_variant 0.4
folC 2746391 p.Val403Ala missense_variant 1.0
folC 2747486 p.Trp38Ser missense_variant 0.33
Rv2752c 3064964 p.Ala410Ser missense_variant 0.67
Rv2752c 3065133 p.Asp353Glu missense_variant 0.25
Rv2752c 3065977 p.Asp72Val missense_variant 0.33
Rv2752c 3067009 c.-818A>G upstream_gene_variant 1.0
thyX 3067223 c.723G>A synonymous_variant 0.33
thyX 3067812 p.Gln45Arg missense_variant 1.0
thyX 3067866 p.Thr27Asn missense_variant 0.22
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
fbiD 3339402 c.285C>A synonymous_variant 0.22
Rv3083 3448551 c.48C>T synonymous_variant 0.25
Rv3083 3449167 p.Ala222Ser missense_variant 0.29
Rv3083 3449359 p.Phe286Leu missense_variant 0.29
Rv3083 3449435 p.Ser311* stop_gained 0.29
Rv3083 3449692 p.Leu397Met missense_variant 0.5
Rv3083 3449757 p.Tyr418* stop_gained 0.33
fprA 3473919 c.-88A>G upstream_gene_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474557 p.Glu184Gly missense_variant 0.29
fprA 3474993 c.987G>T synonymous_variant 0.22
fprA 3475113 c.1107G>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475323 c.1317T>C synonymous_variant 1.0
Rv3236c 3612694 c.423T>C synonymous_variant 1.0
fbiB 3641584 p.Val17Ala missense_variant 1.0
fbiB 3641782 p.Val83Ala missense_variant 0.25
alr 3841468 c.-49_-48insAGC upstream_gene_variant 0.33
alr 3841522 c.-102T>C upstream_gene_variant 0.22
clpC1 4039853 c.852G>A synonymous_variant 1.0
embC 4239793 c.-70A>C upstream_gene_variant 0.22
embC 4240671 p.Thr270Ile missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244154 p.Thr308Ala missense_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244679 p.Ala483Pro missense_variant 0.25
embA 4244701 p.Gly490Val missense_variant 0.33
embA 4244783 c.1551C>A synonymous_variant 0.2
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248923 p.Met804Val missense_variant 0.14
aftB 4267635 p.Arg401Leu missense_variant 0.4
aftB 4268799 c.37delG frameshift_variant 0.22
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
ethA 4327042 p.Asp144Asn missense_variant 1.0
ethR 4327829 p.Pro94Leu missense_variant 0.4
ethA 4328211 c.-738A>G upstream_gene_variant 1.0
whiB6 4338269 p.Gly85Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407800 p.Val135Met missense_variant 1.0
gid 4408214 c.-12G>T upstream_gene_variant 0.33