TB-Profiler result

Run: SRR6045604
Summary

Run ID: SRR6045604

Sample name:

Date: 04-04-2023 12:02:12

Number of reads: 550307

Percentage reads mapped: 99.36

Strain: La3

Drug-resistance: Sensitive

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
La3 M.orygis 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
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 5157 c.-83C>T upstream_gene_variant 0.17
gyrB 5336 p.Tyr33His missense_variant 0.12
gyrB 5480 p.Gly81Ser missense_variant 0.12
gyrB 5516 p.Ile93Val missense_variant 1.0
gyrB 6109 c.870G>A synonymous_variant 1.0
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrB 6717 p.Ile493Thr missense_variant 1.0
gyrA 7190 c.-112C>T upstream_gene_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7763 c.462T>A synonymous_variant 0.18
gyrA 7773 p.Gly158Cys missense_variant 0.18
gyrA 8414 p.Asp371Glu missense_variant 0.17
gyrA 8930 c.1629C>T synonymous_variant 1.0
gyrA 9065 c.1764C>A synonymous_variant 0.12
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9239 c.1938C>T synonymous_variant 0.14
gyrA 9269 c.1968C>T synonymous_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9682 p.Ala794Glu missense_variant 0.14
gyrA 9741 p.Ala814Ser missense_variant 0.18
fgd1 490661 c.-122_-121insGCGAGC upstream_gene_variant 1.0
fgd1 491309 p.Ala176Gly missense_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491749 p.Leu323Phe missense_variant 1.0
mshA 575500 c.153G>T synonymous_variant 0.12
mshA 575533 c.186C>T synonymous_variant 0.17
mshA 575593 c.246G>A synonymous_variant 0.17
mshA 575658 p.Ala104Glu missense_variant 0.13
mshA 576205 c.858G>T synonymous_variant 0.15
mshA 576493 c.1146C>A synonymous_variant 0.33
ccsA 619839 c.-52C>T upstream_gene_variant 0.22
rpoB 760081 p.Asp92Gly missense_variant 0.15
rpoB 760095 p.Met97Val missense_variant 0.14
rpoB 760763 c.957C>A synonymous_variant 0.13
rpoB 761891 c.2085G>T synonymous_variant 0.12
rpoB 761899 p.Asp698Gly missense_variant 0.11
rpoB 762352 c.2557_2562dupGACGAG conservative_inframe_insertion 1.0
rpoB 762555 p.Pro917Ser missense_variant 0.17
rpoB 762801 p.Asp999Asn missense_variant 0.67
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763038 p.Thr1078Ala missense_variant 0.12
rpoC 763490 p.Pro41Ser missense_variant 0.29
rpoC 765252 p.Ser628Ile missense_variant 0.14
rpoC 766503 p.Pro1045Gln missense_variant 0.14
rpoC 767162 p.Asn1265Asp missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775952 c.2529G>T synonymous_variant 0.15
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776103 p.Ile793Gly missense_variant 0.12
mmpL5 776105 c.2376G>C synonymous_variant 0.12
mmpL5 776266 p.Lys739* stop_gained 0.12
mmpL5 777078 p.Ile468Asn missense_variant 0.18
mmpL5 777202 p.Ala427Thr missense_variant 0.15
mmpL5 777496 p.Leu329Met missense_variant 0.14
mmpL5 777746 c.735G>T synonymous_variant 0.12
mmpL5 778086 c.394dupG frameshift_variant 1.0
mmpL5 778219 p.Asp88Tyr missense_variant 0.17
mmpL5 778279 p.Ala68Ser missense_variant 0.13
mmpS5 778604 p.Pro101His missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781465 c.-95G>T upstream_gene_variant 0.17
rplC 801029 p.Gly74Val missense_variant 0.12
fbiC 1302743 c.-188C>G upstream_gene_variant 0.18
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.29
fbiC 1303223 p.Cys98Phe missense_variant 0.14
fbiC 1303656 c.726G>A synonymous_variant 0.18
fbiC 1304524 p.Ala532Ser missense_variant 0.12
Rv1258c 1407249 p.Pro31Gln missense_variant 0.12
embR 1416435 p.Ala305Thr missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.5
rrl 1475539 n.1882A>G non_coding_transcript_exon_variant 1.0
inhA 1673680 c.-522C>G upstream_gene_variant 1.0
fabG1 1673693 p.Leu85Pro missense_variant 0.17
fabG1 1673986 p.Pro183Thr missense_variant 0.18
inhA 1674235 p.Val12Phe missense_variant 0.12
inhA 1674555 c.354G>A synonymous_variant 0.13
inhA 1674696 c.495G>A synonymous_variant 0.12
inhA 1674708 c.507G>A synonymous_variant 0.11
rpsA 1834363 c.822G>A synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917975 c.36C>T synonymous_variant 0.2
tlyA 1918274 p.Asp112Gly missense_variant 0.15
tlyA 1918626 c.687G>A synonymous_variant 0.14
tlyA 1918740 c.801C>A synonymous_variant 0.22
ndh 2101913 p.Ser377Leu missense_variant 0.22
ndh 2102531 p.Leu171Gln missense_variant 0.17
katG 2154707 p.Val469Leu missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155503 c.609C>T synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168975 c.1638C>A synonymous_variant 0.18
PPE35 2169279 c.1312_1333delAACAATGGTGTCTTTTACCGTG frameshift_variant 1.0
PPE35 2169902 c.711G>C synonymous_variant 0.11
PPE35 2170231 p.Gln128Glu missense_variant 0.11
PPE35 2170527 p.Ser29* stop_gained 0.17
PPE35 2170669 c.-57G>A upstream_gene_variant 1.0
Rv1979c 2222063 p.Arg368Trp missense_variant 0.18
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222738 p.Gly143Cys missense_variant 0.13
Rv1979c 2222883 c.282C>T synonymous_variant 0.2
Rv1979c 2223173 c.-9C>A upstream_gene_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289978 c.-737T>G upstream_gene_variant 1.0
pncA 2290233 c.-992C>A upstream_gene_variant 0.17
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518640 p.Glu176* stop_gained 0.18
kasA 2518832 p.Gly240Ser missense_variant 0.17
kasA 2519131 c.1017G>T synonymous_variant 0.17
eis 2714433 p.Asn300Lys missense_variant 0.12
eis 2715095 p.Ala80Ser missense_variant 0.15
eis 2715291 c.42G>A synonymous_variant 0.17
ahpC 2726378 c.186T>A synonymous_variant 1.0
folC 2746391 p.Val403Ala missense_variant 1.0
folC 2746440 p.Val387Leu missense_variant 0.13
ribD 2987318 c.480C>A synonymous_variant 0.4
ribD 2987538 p.Val234Met missense_variant 0.14
Rv2752c 3065254 p.Ser313* stop_gained 0.29
Rv2752c 3065510 p.Gly228Ser missense_variant 0.15
Rv2752c 3065789 p.Arg135Trp missense_variant 0.12
Rv2752c 3065869 p.Thr108Asn missense_variant 0.12
Rv2752c 3065947 p.Gly82Ala missense_variant 0.13
Rv2752c 3065957 c.235T>C synonymous_variant 0.12
Rv2752c 3066066 c.126T>C synonymous_variant 0.11
Rv2752c 3066090 c.101delT frameshift_variant 0.22
Rv2752c 3066346 c.-155C>A upstream_gene_variant 0.12
Rv2752c 3067009 c.-818A>G upstream_gene_variant 1.0
Rv2752c 3067071 c.-880G>A upstream_gene_variant 0.13
thyX 3067297 p.Arg217Ser missense_variant 0.25
thyX 3067812 p.Gln45Arg missense_variant 1.0
thyA 3074196 c.276G>T synonymous_variant 0.17
thyA 3074641 c.-170C>T upstream_gene_variant 0.29
thyA 3074645 c.-174T>G upstream_gene_variant 0.43
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 3339454 p.Leu113Met missense_variant 0.12
Rv3083 3448783 p.Val94Ile missense_variant 1.0
Rv3083 3449217 p.Trp238Cys missense_variant 0.12
Rv3083 3449225 p.Glu241Gly missense_variant 0.11
Rv3083 3449813 p.Asp437Val missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474165 c.159C>G synonymous_variant 0.27
fprA 3475113 c.1107G>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475323 c.1317T>C synonymous_variant 1.0
whiB7 3568626 c.53delT frameshift_variant 0.15
Rv3236c 3612694 c.423T>C synonymous_variant 1.0
fbiA 3641218 p.Val226Ile missense_variant 0.2
fbiA 3641222 p.Pro227His missense_variant 0.2
fbiA 3641255 p.Ala238Glu missense_variant 0.25
fbiB 3641542 p.Gly3Val missense_variant 0.17
fbiB 3641584 p.Val17Ala missense_variant 1.0
fbiB 3642444 p.Ala304Thr missense_variant 0.22
alr 3841131 p.Ala97Glu missense_variant 0.13
rpoA 3877966 p.Thr181Asn missense_variant 0.15
clpC1 4038638 p.Asp689Glu missense_variant 0.22
clpC1 4038747 p.Arg653His missense_variant 0.12
clpC1 4039853 c.852G>A synonymous_variant 1.0
clpC1 4040085 p.Arg207Leu missense_variant 0.17
clpC1 4040144 c.561G>C synonymous_variant 0.11
panD 4044134 p.Asp50Asn missense_variant 1.0
embC 4240496 p.Leu212Met missense_variant 0.22
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240992 p.Ala377Val missense_variant 0.22
embC 4241045 p.Gly395Cys missense_variant 0.33
embC 4241644 c.1782G>T synonymous_variant 0.17
embC 4242317 p.Glu819Lys missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242964 c.-269C>T upstream_gene_variant 0.14
embA 4243243 p.Asp4Gly missense_variant 0.11
embA 4243570 p.Thr113Met missense_variant 0.17
embA 4244154 p.Thr308Ala missense_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embA 4244279 c.1047G>T synonymous_variant 0.25
embA 4244373 p.Pro381Thr missense_variant 0.12
embA 4246392 p.Trp1054Arg missense_variant 0.13
embB 4246516 c.3G>T start_lost 0.12
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4246976 p.Ala155Pro missense_variant 1.0
embB 4247356 c.843C>T synonymous_variant 0.12
embB 4247358 p.Val282Ala missense_variant 0.12
embB 4247374 p.Phe287Leu missense_variant 0.13
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248852 p.Leu780Pro missense_variant 0.17
aftB 4267983 p.Arg285His missense_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
ubiA 4269864 c.-31C>T upstream_gene_variant 0.15
ubiA 4269870 c.-37C>T upstream_gene_variant 0.12
ubiA 4270015 c.-182G>T upstream_gene_variant 0.4
ethA 4327042 p.Asp144Asn missense_variant 1.0
ethA 4327265 p.Thr70Ile missense_variant 0.12
ethR 4327895 p.Ser116Leu missense_variant 0.12
ethR 4327969 p.Phe141Val missense_variant 0.11
ethA 4328211 c.-738A>G upstream_gene_variant 1.0
ethA 4328213 c.-740C>G upstream_gene_variant 0.11
ethA 4328332 c.-859G>A upstream_gene_variant 0.12
whiB6 4338269 p.Gly85Ser missense_variant 1.0
whiB6 4338290 p.Gly78Trp missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407627 c.576C>T synonymous_variant 0.14
gid 4408085 p.Glu40Lys missense_variant 0.12