TB-Profiler result

Run: SRR6045796
Summary

Run ID: SRR6045796

Sample name:

Date: 04-04-2023 12:05:25

Number of reads: 388707

Percentage reads mapped: 50.37

Strain: lineage3.1.2

Drug-resistance: MDR-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
lineage3 East-African-Indian CAS RD750 0.99
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 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 761140 p.His445Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 5605 c.366C>T synonymous_variant 0.5
gyrB 7128 p.Val630Asp missense_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7868 c.567C>T synonymous_variant 0.22
gyrA 8181 p.Gly294Cys missense_variant 0.14
gyrA 8356 p.Val352Glu missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575317 c.-31G>A upstream_gene_variant 0.25
ccsA 619795 c.-96C>T upstream_gene_variant 0.2
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760910 c.1104C>T synonymous_variant 0.17
rpoB 760916 c.1110C>T synonymous_variant 0.2
rpoB 760928 c.1122G>C synonymous_variant 0.18
rpoB 760943 c.1137C>T synonymous_variant 0.18
rpoB 760946 c.1140A>G synonymous_variant 0.18
rpoB 760965 p.Met387Leu missense_variant 0.2
rpoB 760970 c.1164G>C synonymous_variant 0.2
rpoB 760973 c.1167G>T synonymous_variant 0.17
rpoB 760982 c.1176G>C synonymous_variant 0.2
rpoB 760985 c.1179G>C synonymous_variant 0.2
rpoB 760988 c.1182C>G synonymous_variant 0.2
rpoB 760991 c.1185G>T synonymous_variant 0.2
rpoB 760997 c.1191G>C synonymous_variant 0.22
rpoB 761006 c.1200C>G synonymous_variant 0.2
rpoB 761015 c.1209G>C synonymous_variant 0.22
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764407 p.Arg346Ser missense_variant 0.13
rpoC 765211 c.1842G>T synonymous_variant 0.17
rpoC 766642 c.3273C>T synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776371 p.Gly704Ser missense_variant 0.11
mmpL5 776940 p.Tyr514Phe missense_variant 0.13
mmpL5 778179 p.Leu101Pro missense_variant 0.25
mmpS5 779535 c.-631delG upstream_gene_variant 0.29
mmpS5 779684 c.-779C>T upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303351 p.Lys141* stop_gained 0.15
fbiC 1305110 p.Arg727His missense_variant 0.12
Rv1258c 1406242 p.Ala367Thr missense_variant 1.0
embR 1416676 c.672G>A synonymous_variant 1.0
embR 1417256 p.Gly31Asp missense_variant 0.17
atpE 1461120 p.Ile26Phe missense_variant 0.33
atpE 1461167 c.123G>A synonymous_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673242 c.-198C>T upstream_gene_variant 0.15
fabG1 1674009 p.Met190Ile missense_variant 0.33
inhA 1674667 p.Pro156Ser missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918104 c.165G>A synonymous_variant 1.0
ndh 2102186 p.Gly286Asp missense_variant 0.17
ndh 2102823 p.Val74Ile missense_variant 0.12
ndh 2103215 c.-173C>G upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155235 c.877C>T synonymous_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168459 c.2154C>T synonymous_variant 0.11
PPE35 2168604 p.Pro670Leu missense_variant 1.0
PPE35 2168920 p.Val565Ile missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2290178 c.-937A>C upstream_gene_variant 0.2
kasA 2518588 c.478delG frameshift_variant 0.11
eis 2714396 p.Glu313Lys missense_variant 0.18
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.33
folC 2746438 c.1161G>A synonymous_variant 0.13
pepQ 2859478 p.Gly314Asp missense_variant 0.14
ribD 2986876 p.Pro13Leu missense_variant 0.15
Rv2752c 3065020 p.Arg391His missense_variant 0.11
Rv2752c 3065117 p.Gly359Ser missense_variant 0.18
Rv2752c 3066029 p.Pro55Ser missense_variant 0.18
Rv2752c 3066084 p.His36Gln missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338964 c.-154G>A upstream_gene_variant 0.12
Rv3083 3448597 p.Ile32Val missense_variant 0.11
Rv3083 3449814 p.Asp437Glu missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3613003 c.114G>A synonymous_variant 0.25
fbiA 3640356 c.-187G>A upstream_gene_variant 0.11
fbiA 3640407 c.-136G>A upstream_gene_variant 0.17
fbiA 3640987 p.Arg149Cys missense_variant 0.14
fbiA 3641425 p.His295Asn missense_variant 0.11
fbiB 3642344 c.810G>A synonymous_variant 1.0
alr 3840292 p.Gln377* stop_gained 0.12
alr 3840883 p.Arg180Ser missense_variant 0.12
rpoA 3878333 p.Val59Leu missense_variant 0.11
ddn 3987022 p.Arg60Gln missense_variant 0.14
embC 4240014 p.Pro51Leu missense_variant 0.25
embC 4240147 c.285C>A synonymous_variant 0.18
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242586 c.-647C>T upstream_gene_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242736 c.-497C>T upstream_gene_variant 0.12
embC 4242740 p.Leu960Ile missense_variant 0.12
embB 4249603 c.3090C>T synonymous_variant 0.12
aftB 4267612 p.Asp409Asn missense_variant 0.17
ubiA 4269943 c.-111dupG upstream_gene_variant 0.14
ethR 4326660 c.-889G>A upstream_gene_variant 0.12
ethA 4327307 p.Asp56Gly missense_variant 0.11
whiB6 4338494 p.Thr10Ala missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338684 c.-163C>T upstream_gene_variant 0.18
gid 4407575 p.Gln210Lys missense_variant 0.14
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407956 p.Arg83Gly missense_variant 1.0
gid 4408217 c.-15C>T upstream_gene_variant 0.12