TB-Profiler result

Run: SRR10993937

Summary

Run ID: SRR10993937

Sample name:

Date: 02-04-2023 19:48:36

Number of reads: 265901

Percentage reads mapped: 99.47

Strain: La1.6

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
La1.6 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 5494 c.255G>A synonymous_variant 0.14
gyrB 5752 c.513G>A synonymous_variant 1.0
gyrB 5994 p.His252Pro missense_variant 0.14
gyrA 6406 c.-896C>T upstream_gene_variant 1.0
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrA 7042 c.-260C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8205 p.Ile302Val missense_variant 0.14
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 491014 p.Thr78Pro missense_variant 0.27
fgd1 491735 p.Arg318Leu missense_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620532 c.642T>G synonymous_variant 0.33
ccsA 620768 p.Ala293Gly missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763363 c.-7G>A upstream_gene_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777766 p.Gly239Trp missense_variant 0.29
mmpS5 778607 p.Ala100Asp missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1304924 p.Pro665Gln missense_variant 0.2
Rv1258c 1406255 p.Leu362Phe missense_variant 0.13
Rv1258c 1407392 c.-52G>A upstream_gene_variant 1.0
embR 1417449 c.-102C>T upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476022 n.2365A>G non_coding_transcript_exon_variant 1.0
rrl 1476574 n.2917A>C non_coding_transcript_exon_variant 0.25
inhA 1674588 c.387G>C synonymous_variant 0.25
rpsA 1833841 c.300C>A synonymous_variant 0.2
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103142 c.-100A>G upstream_gene_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2153976 c.2136C>T synonymous_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154885 c.1227C>T synonymous_variant 0.25
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2155743 c.369G>T synonymous_variant 0.2
katG 2156025 c.87C>A synonymous_variant 1.0
katG 2156367 c.-256G>A upstream_gene_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 2169346 c.1266delC frameshift_variant 0.2
PPE35 2169356 c.1257C>T synonymous_variant 0.22
PPE35 2169844 p.Ile257Val missense_variant 0.29
PPE35 2170669 c.-57G>T upstream_gene_variant 0.2
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222935 p.Ala77Val missense_variant 1.0
Rv1979c 2223062 p.Thr35Ala missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518590 p.Gly159Val missense_variant 0.4
ahpC 2726179 c.-14T>C upstream_gene_variant 0.17
folC 2746245 p.Ala452Thr missense_variant 1.0
folC 2747117 p.Ala161Glu missense_variant 0.33
ribD 2987615 c.777A>G stop_lost&splice_region_variant 1.0
Rv2752c 3065834 p.Arg120Ser missense_variant 0.15
Rv2752c 3066239 c.-48G>T 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 3086931 p.Gly38Cys missense_variant 0.25
ald 3087084 c.266delA frameshift_variant 1.0
ald 3087677 c.858G>T synonymous_variant 0.12
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
Rv3236c 3612338 p.Arg260Leu missense_variant 0.22
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4039931 c.774T>G synonymous_variant 0.29
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241955 p.Ala698Gly missense_variant 0.2
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 0.92
embA 4245195 p.Ile655Val missense_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
embB 4247791 c.1278C>T synonymous_variant 1.0
embB 4249027 c.2514T>C synonymous_variant 0.14
aftB 4267417 p.Pro474Thr missense_variant 0.25
aftB 4269342 c.-506G>A upstream_gene_variant 0.2
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