TB-Profiler result

Run: SRR8886988
Summary

Run ID: SRR8886988

Sample name:

Date: 04-04-2023 22:01:58

Number of reads: 541313

Percentage reads mapped: 98.85

Strain: La1.2.BCG

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
La1.2 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
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
mshA 575186 c.-161delG upstream_gene_variant 0.13
mshA 576591 p.Arg415Leu missense_variant 0.21
rpoB 761821 p.Ser672Tyr missense_variant 0.14
rpoB 761891 c.2085G>T synonymous_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763355 c.-15G>T upstream_gene_variant 0.17
rpoC 763575 p.Arg69Pro missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 778722 p.Gly62Cys missense_variant 0.17
mmpR5 779449 p.Leu154Met missense_variant 0.14
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
Rv1258c 1407010 p.Ala111Ser missense_variant 0.13
embR 1417011 p.Gly113Trp missense_variant 0.16
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473882 n.225A>G non_coding_transcript_exon_variant 0.15
rrl 1474635 n.978C>A non_coding_transcript_exon_variant 0.15
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 2102731 c.312C>A synonymous_variant 0.17
ndh 2103034 c.9C>A synonymous_variant 0.15
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154153 c.1959G>T synonymous_variant 0.17
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 2167931 c.2682C>A synonymous_variant 0.33
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168028 p.Pro862His missense_variant 0.15
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2168920 p.Val565Phe missense_variant 0.97
pncA 2289846 c.-605C>A upstream_gene_variant 0.2
pncA 2289960 c.-719C>A upstream_gene_variant 0.18
kasA 2518132 c.18C>T synonymous_variant 1.0
folC 2746835 p.Ser255* stop_gained 0.18
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 3339364 p.Pro83Thr missense_variant 0.15
fbiD 3339480 p.Gln121His missense_variant 0.15
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
fbiB 3642627 p.Arg365Ser missense_variant 0.17
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
embC 4242669 p.Ile936Thr missense_variant 0.11
embC 4242672 p.Pro937Gln missense_variant 0.24
embC 4242837 p.Pro992His missense_variant 0.17
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4245088 c.1859delG frameshift_variant 0.13
embA 4245934 p.Pro901Gln missense_variant 0.17
embB 4246551 p.Asn13Ser missense_variant 0.93
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 4249616 p.Gly1035Cys missense_variant 0.18
aftB 4267513 p.Leu442Phe missense_variant 0.13
aftB 4267737 c.1099delA frameshift_variant 0.13
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4268672 c.165C>A synonymous_variant 0.2
aftB 4268684 p.Gln51His missense_variant 0.18
aftB 4268873 c.-37C>A upstream_gene_variant 0.17
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
ubiA 4270017 c.-184G>T upstream_gene_variant 0.18
ethA 4328133 c.-660C>A upstream_gene_variant 0.17
ethA 4328175 c.-702G>T upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
Rv1979c 2208006 c.-8682_*13712del transcript_ablation 1.0
Rv1979c 2221058 c.-8682_*660del transcript_ablation 1.0