TB-Profiler result

Run: ERR4817396
Summary

Run ID: ERR4817396

Sample name:

Date: 01-04-2023 14:58:12

Number of reads: 1187308

Percentage reads mapped: 99.49

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 761095 p.Leu430Pro missense_variant 1.0 rifampicin
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
gyrB 6076 c.837C>T synonymous_variant 0.12
gyrB 6285 p.Asp349Val missense_variant 0.13
gyrA 6406 c.-896C>T upstream_gene_variant 1.0
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrA 6907 c.-395C>T upstream_gene_variant 0.13
gyrB 6929 p.Ala564Thr missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8106 p.Leu269Met missense_variant 0.14
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
gyrA 9648 p.Val783Met missense_variant 0.11
fgd1 490831 p.Pro17Thr missense_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 761952 p.Ala716Ser missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763459 p.Lys30Asn missense_variant 0.12
rpoC 763462 c.93G>T synonymous_variant 0.12
rpoC 763575 p.Arg69Pro missense_variant 1.0
rpoC 763582 p.Lys71Asn missense_variant 0.13
rpoC 763661 p.Ala98Thr missense_variant 0.15
rpoC 766740 p.Val1124Ala missense_variant 0.11
rpoC 767063 p.Val1232Met missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 778481 p.Ala142Glu missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781568 c.9C>T synonymous_variant 1.0
rplC 801251 p.Pro148Leu missense_variant 0.2
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1304938 p.Glu670Lys missense_variant 0.12
embR 1416286 p.His354Gln missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476008 n.2351A>G non_coding_transcript_exon_variant 1.0
fabG1 1674007 p.Met190Val missense_variant 0.18
inhA 1674280 c.82dupG frameshift_variant 0.29
inhA 1674599 p.Ala133Glu missense_variant 0.12
inhA 1674601 p.Leu134Met missense_variant 0.12
inhA 1674814 p.Gly205Arg missense_variant 0.12
rpsA 1833621 p.Asp27Gly missense_variant 0.11
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 2102316 p.Ile243Val missense_variant 0.11
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 1.0
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2168920 p.Val565Phe missense_variant 1.0
pncA 2289960 c.-719C>A upstream_gene_variant 0.14
pncA 2290168 c.-927G>T upstream_gene_variant 0.2
kasA 2518132 c.18C>T synonymous_variant 1.0
Rv2752c 3064813 p.Ile460Asn missense_variant 0.12
Rv2752c 3065022 c.1170G>A synonymous_variant 0.12
Rv2752c 3067080 c.-889G>C upstream_gene_variant 0.11
ald 3086670 c.-150G>A upstream_gene_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
ald 3087601 p.Gly261Val missense_variant 0.14
Rv3083 3448422 c.-82T>C upstream_gene_variant 0.11
Rv3083 3448745 p.Ile81Ser missense_variant 1.0
Rv3083 3448783 p.Val94Ile missense_variant 1.0
Rv3083 3448866 c.363G>A synonymous_variant 0.12
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
Rv3236c 3612816 p.Ala101Ser missense_variant 0.14
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
rpoA 3878666 c.-159C>A upstream_gene_variant 0.22
ddn 3987237 p.Ser132Gly missense_variant 0.18
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4039613 c.1092C>T synonymous_variant 0.11
clpC1 4039649 c.1056G>T synonymous_variant 0.12
clpC1 4039771 p.Leu312Phe missense_variant 0.12
clpC1 4040163 p.Ala181Glu missense_variant 0.11
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 4243151 c.-82T>C upstream_gene_variant 0.11
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
embB 4248234 p.Leu574Pro missense_variant 0.11
embB 4249529 p.Ile1006Val missense_variant 0.11
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
ethR 4327090 c.-459G>A upstream_gene_variant 0.12
ethA 4327400 p.Asp25Gly missense_variant 0.14
ethR 4327699 p.Ala51Ser missense_variant 0.11
ethA 4327809 c.-336T>C upstream_gene_variant 0.14
ethR 4328155 p.Leu203Met missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
Rv1979c 2221058 c.-8682_*660del transcript_ablation 1.0