TB-Profiler result

Run: SRR13986563

Summary

Run ID: SRR13986563

Sample name:

Date: 03-04-2023 09:43:49

Number of reads: 533887

Percentage reads mapped: 95.15

Strain: La1.7.1

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 0.97
La1.7 M.bovis None None 1.0
La1.7.1 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 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 575514 p.Pro56Gln missense_variant 0.15
ccsA 620732 p.Ala281Val missense_variant 0.14
rpoB 761112 p.Gln436* stop_gained 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764512 c.1143G>T synonymous_variant 0.14
rpoC 765803 p.Thr812Pro missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777366 p.Arg372Leu missense_variant 0.13
mmpR5 778082 c.-908T>C upstream_gene_variant 0.18
mmpR5 778088 c.-902C>G upstream_gene_variant 0.25
mmpR5 778094 c.-896A>G upstream_gene_variant 0.17
mmpL5 778219 p.Asp88His missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1304826 c.1900delT frameshift_variant 0.12
fbiC 1304900 p.Arg657His missense_variant 0.25
fbiC 1304922 c.1992C>T synonymous_variant 0.22
fbiC 1305235 p.Val769Leu missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673690 p.Val84Ala missense_variant 0.17
rpsA 1833452 c.-90C>G upstream_gene_variant 1.0
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101839 p.Ala402Thr missense_variant 0.12
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2153940 p.Phe724Leu missense_variant 0.18
katG 2154683 p.Trp477Arg missense_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154897 c.1215C>A synonymous_variant 0.13
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
PPE35 2170133 c.480G>A synonymous_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
folC 2746851 p.Val250Leu missense_variant 0.18
folC 2747338 c.261C>A synonymous_variant 0.2
Rv2752c 3064537 p.Val552Ala missense_variant 0.15
Rv2752c 3065277 c.915C>T synonymous_variant 0.13
thyA 3074645 c.-174T>G upstream_gene_variant 0.29
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
Rv3083 3449650 p.Asn383Asp missense_variant 0.11
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 3612595 c.522A>G synonymous_variant 0.12
fbiB 3642478 p.Asp315Ala missense_variant 1.0
alr 3840976 p.Gly149Ser missense_variant 0.12
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
ddn 3986858 c.15G>T synonymous_variant 0.13
ddn 3987048 p.Asp69His missense_variant 0.13
clpC1 4038403 c.2302T>C synonymous_variant 1.0
embC 4240443 p.Arg194Leu missense_variant 0.18
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240768 c.906G>A synonymous_variant 0.2
embC 4241665 c.1803G>T synonymous_variant 0.12
embC 4241767 c.1905C>A synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4243666 p.Thr145Ile missense_variant 0.11
embA 4244033 c.801C>T synonymous_variant 0.18
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4245157 p.Ala642Asp missense_variant 0.14
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247165 p.Lys218* stop_gained 0.14
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248735 p.Arg741Leu missense_variant 0.14
aftB 4267178 c.1659C>T synonymous_variant 0.13
aftB 4267858 p.Ile327Val missense_variant 1.0
ubiA 4269052 p.Arg261His 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
gid 4408334 c.-132G>T upstream_gene_variant 0.12