TB-Profiler result

Run: ERR4627311
Summary

Run ID: ERR4627311

Sample name:

Date: 01-04-2023 06:30:49

Number of reads: 1108981

Percentage reads mapped: 65.71

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 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
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 8048 c.747C>A synonymous_variant 1.0
gyrA 8285 c.984C>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
mshA 576410 p.Phe355Leu missense_variant 0.1
mshA 576446 p.Thr367Pro missense_variant 0.25
mshA 576616 c.1269G>C synonymous_variant 0.25
rpoC 762863 c.-507T>C upstream_gene_variant 0.14
rpoB 762879 p.Met1025Leu missense_variant 0.11
rpoC 762923 c.-447C>G upstream_gene_variant 0.12
rpoB 762925 p.Thr1040Ile missense_variant 0.12
rpoB 762939 p.Met1045Leu missense_variant 0.12
rpoB 762942 p.Ile1046Val missense_variant 0.12
rpoC 762947 c.-423C>G upstream_gene_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763101 p.Ala1099Thr missense_variant 0.12
rpoB 763151 p.Phe1115Leu missense_variant 0.17
rpoC 764535 p.Arg389Pro missense_variant 0.17
rpoC 765297 p.Pro643Leu missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777305 c.1176C>A synonymous_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801114 c.306C>G synonymous_variant 0.12
rplC 801454 p.Glu216Gln missense_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1305047 p.Ser706* stop_gained 0.22
Rv1258c 1407175 c.166T>C synonymous_variant 0.12
Rv1258c 1407220 c.118_120delAGC conservative_inframe_deletion 0.11
embR 1416527 p.Val274Ala missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471935 n.90T>C non_coding_transcript_exon_variant 1.0
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.2
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.2
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.19
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.19
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.24
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.29
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.17
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.11
rrl 1474806 n.1149A>C non_coding_transcript_exon_variant 0.11
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.11
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.11
rrl 1474853 n.1196A>G non_coding_transcript_exon_variant 0.11
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.12
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.16
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.17
rrl 1476381 n.2724G>T non_coding_transcript_exon_variant 0.23
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.35
rrl 1476384 n.2727G>A non_coding_transcript_exon_variant 0.16
rrl 1476405 n.2748C>T non_coding_transcript_exon_variant 0.22
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.22
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.44
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.24
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.3
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.33
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.3
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.32
rrl 1476473 n.2816G>A non_coding_transcript_exon_variant 0.17
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.29
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.12
rrl 1476492 n.2835G>A non_coding_transcript_exon_variant 0.12
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.18
rrl 1476561 n.2904C>A non_coding_transcript_exon_variant 0.22
rrl 1476728 n.3071T>A non_coding_transcript_exon_variant 0.2
fabG1 1673553 p.Asp38Glu missense_variant 0.23
inhA 1673715 c.-487C>G upstream_gene_variant 1.0
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918052 p.Pro38Arg missense_variant 0.18
tlyA 1918618 p.Ala227Pro missense_variant 0.16
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 2168265 p.Gly783Val missense_variant 0.12
PPE35 2168319 p.Thr765Ile missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2170024 p.Thr197Ser missense_variant 0.12
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
kasA 2518512 c.403delC frameshift_variant 0.2
eis 2715125 p.Thr70Ala missense_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.2
thyX 3067311 c.634delG frameshift_variant 0.12
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 3339734 p.Ala206Gly missense_variant 0.33
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
alr 3841069 p.Ile118Val missense_variant 0.1
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4039566 p.Val380Gly missense_variant 0.15
embC 4240409 p.Pro183Ala missense_variant 0.25
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4242642 p.Arg927His missense_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4243251 p.Glu7Lys missense_variant 0.12
embA 4244220 c.988C>T synonymous_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.25
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4246949 c.438delA frameshift_variant 0.11
embB 4247016 p.Ser168Trp missense_variant 0.33
embB 4247020 c.507C>G synonymous_variant 0.4
embB 4247028 p.Leu172Arg missense_variant 0.67
embB 4247484 p.Gly324Val missense_variant 0.17
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248734 p.Arg741Trp missense_variant 1.0
embB 4249527 p.Gly1005Val missense_variant 0.15
aftB 4267167 p.Gln557Pro missense_variant 1.0
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4268453 c.384G>T synonymous_variant 0.14
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 4326024 p.Pro484Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0