TB-Profiler result

Run: ERR3439441
Summary

Run ID: ERR3439441

Sample name:

Date: 01-04-2023 02:07:15

Number of reads: 693367

Percentage reads mapped: 70.01

Strain: La1.8.1

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
La1 M.bovis None None 1.0
La1.8 M.bovis None None 1.0
La1.8.1 M.bovis None 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
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 8741 c.1440C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9217 p.Asp639Ala missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620713 p.Tyr275His missense_variant 0.96
rpoB 762185 c.2379G>C synonymous_variant 0.14
rpoB 762308 c.2502G>T synonymous_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764827 c.1458G>C synonymous_variant 0.18
rpoC 764858 c.1489T>C synonymous_variant 0.18
rpoC 764869 c.1500C>T synonymous_variant 0.19
rpoC 764872 c.1503A>G synonymous_variant 0.19
rpoC 764887 c.1518G>C synonymous_variant 0.16
rpoC 764888 c.1519T>C synonymous_variant 0.16
rpoC 764911 c.1542A>G synonymous_variant 0.19
rpoC 764912 p.Met515Leu missense_variant 0.19
rpoC 764920 c.1551G>C synonymous_variant 0.2
rpoC 764935 c.1566T>C synonymous_variant 0.21
rpoC 764947 c.1578G>C synonymous_variant 0.2
rpoC 764948 c.1579_1581delTTGinsCTC synonymous_variant 0.2
rpoC 764968 c.1599T>C synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.2
rrs 1472416 n.571C>T non_coding_transcript_exon_variant 0.18
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.18
rrs 1472426 n.581T>C non_coding_transcript_exon_variant 0.17
rrs 1472431 n.586G>A non_coding_transcript_exon_variant 0.17
rrs 1472435 n.590T>C non_coding_transcript_exon_variant 0.17
rrs 1472437 n.592T>A non_coding_transcript_exon_variant 0.17
rrs 1472439 n.594C>T non_coding_transcript_exon_variant 0.17
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.15
rrs 1472449 n.604C>T non_coding_transcript_exon_variant 0.14
rrs 1472450 n.605A>G non_coding_transcript_exon_variant 0.14
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.13
rrs 1472456 n.611T>C non_coding_transcript_exon_variant 0.13
rrs 1472462 n.617T>C non_coding_transcript_exon_variant 0.13
rrs 1472463 n.618G>A non_coding_transcript_exon_variant 0.13
rrs 1472467 n.622G>T non_coding_transcript_exon_variant 0.13
rrs 1472471 n.626G>A non_coding_transcript_exon_variant 0.13
rrs 1472473 n.628G>T non_coding_transcript_exon_variant 0.13
rrs 1472497 n.652G>T non_coding_transcript_exon_variant 0.12
rrs 1472580 n.735C>A non_coding_transcript_exon_variant 0.25
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.31
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.31
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.33
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.33
rrs 1472836 n.991G>A non_coding_transcript_exon_variant 0.14
rrs 1472840 n.995A>C non_coding_transcript_exon_variant 0.13
rrs 1472849 n.1004C>A non_coding_transcript_exon_variant 0.13
rrs 1472858 n.1013G>T non_coding_transcript_exon_variant 0.15
rrs 1472860 n.1015C>G non_coding_transcript_exon_variant 0.15
rrs 1472861 n.1016G>C non_coding_transcript_exon_variant 0.15
rrs 1472862 n.1017T>C non_coding_transcript_exon_variant 0.15
rrs 1472863 n.1018T>C non_coding_transcript_exon_variant 0.15
rrs 1472873 n.1028C>T non_coding_transcript_exon_variant 0.15
rrs 1472875 n.1030T>G non_coding_transcript_exon_variant 0.15
rrs 1472880 n.1035G>A non_coding_transcript_exon_variant 0.18
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 0.25
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.33
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.3
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.22
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.15
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.5
rrl 1473814 n.157A>G non_coding_transcript_exon_variant 0.5
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.5
rrl 1473832 n.175C>T non_coding_transcript_exon_variant 0.38
rrl 1473833 n.176_177insT non_coding_transcript_exon_variant 0.33
rrl 1473844 n.187C>T non_coding_transcript_exon_variant 0.25
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.4
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 0.4
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.33
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.33
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.33
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.43
rrl 1475443 n.1786G>A non_coding_transcript_exon_variant 0.38
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.38
rrl 1475460 n.1803A>G non_coding_transcript_exon_variant 0.38
rrl 1475475 n.1818C>T non_coding_transcript_exon_variant 0.3
rrl 1475479 n.1822C>T non_coding_transcript_exon_variant 0.3
rrl 1475480 n.1823A>T non_coding_transcript_exon_variant 0.3
rrl 1475481 n.1824C>G non_coding_transcript_exon_variant 0.3
rrl 1475482 n.1825A>G non_coding_transcript_exon_variant 0.3
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.3
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.33
rrl 1475531 n.1874C>T non_coding_transcript_exon_variant 0.33
rrl 1475538 n.1881T>A non_coding_transcript_exon_variant 0.38
rrl 1475539 n.1882A>T non_coding_transcript_exon_variant 0.33
rrl 1475550 n.1893A>G non_coding_transcript_exon_variant 0.33
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.25
rrl 1475735 n.2078T>C non_coding_transcript_exon_variant 0.29
rrl 1475750 n.2093A>C non_coding_transcript_exon_variant 0.8
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.2
rrl 1475758 n.2101A>G non_coding_transcript_exon_variant 0.2
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.18
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.18
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.22
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.22
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.29
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.29
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.25
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.25
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.4
rrl 1476088 n.2431A>C non_coding_transcript_exon_variant 0.4
rrl 1476099 n.2442A>G non_coding_transcript_exon_variant 0.33
rrl 1476105 n.2450delA non_coding_transcript_exon_variant 0.29
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.33
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.33
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.4
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.33
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.29
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.29
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.29
rrl 1476300 n.2643G>A non_coding_transcript_exon_variant 0.29
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.33
rpsA 1833961 c.420C>G synonymous_variant 0.11
rpsA 1833979 c.438T>C synonymous_variant 0.11
rpsA 1833985 c.444G>C synonymous_variant 0.12
rpsA 1833988 c.447C>G synonymous_variant 0.11
rpsA 1833991 c.450C>G synonymous_variant 0.11
rpsA 1834000 c.459G>C synonymous_variant 0.11
rpsA 1834012 c.471G>T synonymous_variant 0.12
rpsA 1834015 c.474G>C synonymous_variant 0.12
rpsA 1834024 c.483G>C synonymous_variant 0.11
rpsA 1834030 c.489C>G synonymous_variant 0.11
rpsA 1834034 p.Ile165Val missense_variant 0.12
rpsA 1834069 c.528G>C synonymous_variant 0.11
rpsA 1834340 p.Met267Leu missense_variant 0.15
rpsA 1834423 c.882G>T synonymous_variant 0.14
rpsA 1834451 c.910T>C synonymous_variant 0.15
rpsA 1834468 c.927A>G synonymous_variant 0.14
rpsA 1834474 c.933C>G synonymous_variant 0.14
rpsA 1834483 c.942G>A synonymous_variant 0.14
rpsA 1834528 c.987T>C synonymous_variant 0.12
rpsA 1834540 c.999G>C synonymous_variant 0.12
rpsA 1834543 c.1002C>G synonymous_variant 0.12
rpsA 1834546 c.1005T>C synonymous_variant 0.12
rpsA 1834552 c.1011G>T synonymous_variant 0.12
rpsA 1834555 c.1014T>C synonymous_variant 0.15
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102193 p.Arg284Trp 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
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168319 p.Thr765Ile missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715125 p.Thr70Ala missense_variant 1.0
ahpC 2726675 c.483A>G synonymous_variant 0.12
ahpC 2726681 c.489A>G synonymous_variant 0.13
ahpC 2726687 c.495C>G synonymous_variant 0.12
ahpC 2726693 c.501C>G synonymous_variant 0.12
ahpC 2726696 c.504C>G synonymous_variant 0.13
ahpC 2726717 c.525A>C synonymous_variant 0.12
Rv2752c 3065988 p.Glu68Asp missense_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 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
clpC1 4038905 c.1800A>C synonymous_variant 0.12
clpC1 4038908 c.1797C>G synonymous_variant 0.12
clpC1 4038911 c.1794G>T synonymous_variant 0.12
clpC1 4038914 c.1791G>C synonymous_variant 0.12
clpC1 4038917 c.1788C>T synonymous_variant 0.12
clpC1 4038923 c.1782A>G synonymous_variant 0.12
clpC1 4038926 c.1779G>T synonymous_variant 0.12
clpC1 4038932 c.1773G>C synonymous_variant 0.13
clpC1 4038941 c.1764G>C synonymous_variant 0.14
clpC1 4038953 c.1752A>G synonymous_variant 0.13
clpC1 4038956 c.1749T>C synonymous_variant 0.12
clpC1 4038971 c.1734T>C synonymous_variant 0.11
clpC1 4038974 c.1731T>C synonymous_variant 0.11
clpC1 4038986 p.Asp573Glu missense_variant 0.13
clpC1 4038989 c.1716T>C synonymous_variant 0.14
clpC1 4038997 c.1708T>C synonymous_variant 0.14
clpC1 4039004 c.1701C>G synonymous_variant 0.21
clpC1 4039865 c.840T>C synonymous_variant 0.12
clpC1 4039886 c.819C>G synonymous_variant 0.12
clpC1 4039898 c.807C>G synonymous_variant 0.12
clpC1 4039952 c.753T>C synonymous_variant 0.1
clpC1 4039955 c.750G>C synonymous_variant 0.1
clpC1 4039958 c.747G>C synonymous_variant 0.1
clpC1 4039979 c.726C>G synonymous_variant 0.11
embC 4240671 p.Thr270Ile missense_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 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4268184 p.Gly218Glu missense_variant 0.12
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
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0