TB-Profiler result

Run: SRR18391712
Summary

Run ID: SRR18391712

Sample name:

Date: 03-04-2023 19:40:50

Number of reads: 332268

Percentage reads mapped: 97.41

Strain: La1.7.1

Drug-resistance: Other

Download CSV Download TXT Download PDF Download JSON
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
La1.7 M.bovis None None 0.99
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 575853 p.Trp169* stop_gained 0.4
mshA 576393 p.Pro349Leu missense_variant 0.2
rpoB 762678 p.Leu958Ile missense_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764269 c.900G>C synonymous_variant 0.11
rpoC 766745 p.Gly1126Cys missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778100 c.380delA frameshift_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.29
fbiC 1303166 p.Ser79Ile missense_variant 0.13
fbiC 1304551 p.Gly541Ser missense_variant 0.18
fbiC 1304832 c.1902C>G synonymous_variant 0.12
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 1.0
Rv1258c 1406532 p.Gly270Val missense_variant 0.11
Rv1258c 1407047 c.294C>A synonymous_variant 0.17
Rv1258c 1407338 c.3G>T start_lost 0.17
embR 1416366 p.His328Tyr missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834830 p.Ala430Glu missense_variant 0.12
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917836 c.-104C>A upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102538 p.Lys169Gln missense_variant 0.25
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 2167745 p.Thr956Arg missense_variant 0.13
PPE35 2167760 c.2853G>A synonymous_variant 0.12
PPE35 2167763 p.Ile950Val missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168259 p.Thr785Met missense_variant 0.18
PPE35 2168319 p.Thr765Ile missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.15
PPE35 2169910 p.Asn235Tyr missense_variant 0.15
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222555 p.Pro204Thr missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289912 c.-671G>T upstream_gene_variant 0.14
pncA 2290062 c.-821G>A upstream_gene_variant 0.22
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518992 p.Arg293Leu missense_variant 0.12
ahpC 2726759 c.567A>G synonymous_variant 0.11
folC 2746524 p.Ala359Thr missense_variant 0.13
pepQ 2860518 c.-100C>G upstream_gene_variant 0.13
pepQ 2860594 c.-176C>A upstream_gene_variant 0.12
ribD 2986976 c.138C>T synonymous_variant 0.17
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 3338957 c.-161C>T upstream_gene_variant 0.11
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 3612047 p.Ala357Val missense_variant 0.14
Rv3236c 3612242 p.Pro292Leu missense_variant 0.13
fbiA 3640636 p.Ser32Pro missense_variant 1.0
fbiA 3641270 p.Tyr243Cys missense_variant 0.11
fbiB 3642040 p.Gly169Val missense_variant 0.13
fbiB 3642478 p.Asp315Ala missense_variant 1.0
rpoA 3878285 p.Glu75Lys missense_variant 0.13
rpoA 3878332 p.Val59Glu missense_variant 0.11
ddn 3986713 c.-131C>A upstream_gene_variant 0.22
ddn 3987021 c.178C>A synonymous_variant 0.17
clpC1 4038403 c.2302T>C synonymous_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241468 p.Ala536Ser missense_variant 0.15
embC 4241791 c.1929G>A synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4242985 c.-248C>T upstream_gene_variant 0.17
embA 4243830 p.Gly200Cys missense_variant 0.12
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4245310 p.Val693Asp missense_variant 0.12
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246710 p.Ser66Asn missense_variant 0.25
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247058 p.Arg182His missense_variant 0.17
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247870 p.Ala453Ser missense_variant 0.11
embB 4249758 p.Thr1082Ser missense_variant 0.12
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4268621 p.Trp72Cys missense_variant 0.29
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
ethR 4327631 p.Ala28Glu missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407679 p.Arg175Leu missense_variant 0.12
gid 4407761 p.Trp148Arg missense_variant 0.15
gid 4408398 c.-196C>A upstream_gene_variant 0.11
fbiC 1305494 c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN frameshift_variant&stop_lost&splice_region_variant 1.0