TB-Profiler result

Run: SRR5535705
Summary

Run ID: SRR5535705

Sample name:

Date: 04-04-2023 10:38:32

Number of reads: 1040120

Percentage reads mapped: 99.26

Strain:

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
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 5167 c.-73C>T upstream_gene_variant 0.15
gyrB 5707 c.468G>T synonymous_variant 0.4
gyrB 5806 c.567C>A synonymous_variant 0.2
gyrA 6475 c.-827C>A upstream_gene_variant 0.25
gyrA 6589 c.-713G>A upstream_gene_variant 0.4
gyrB 6782 p.Asp515His missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7538 p.Glu79Asp missense_variant 0.17
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7725 p.Leu142Met missense_variant 0.25
gyrA 8123 p.Leu274Phe missense_variant 0.67
gyrA 8960 p.Asp553Glu missense_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491660 p.Ala293Asp missense_variant 0.4
fgd1 491719 p.Pro313Thr missense_variant 0.5
mshA 575360 p.Arg5Trp missense_variant 0.15
mshA 575907 p.Ala187Val missense_variant 0.86
mshA 575946 p.Thr200Met missense_variant 0.25
ccsA 620506 p.Pro206Thr missense_variant 0.67
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759947 c.141C>A synonymous_variant 0.5
rpoB 760177 p.Ala124Val missense_variant 0.2
rpoB 760394 c.588C>A synonymous_variant 0.25
rpoB 760648 p.Pro281Leu missense_variant 0.5
rpoB 762321 p.Gly839Ser missense_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766244 c.2876delA frameshift_variant 0.29
rpoC 767053 p.Glu1228Asp missense_variant 0.22
rpoC 767088 p.Cys1240Phe missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776002 p.Leu827Met missense_variant 0.5
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776204 c.2277C>A synonymous_variant 0.4
mmpL5 776498 c.1983G>A synonymous_variant 0.33
mmpL5 777697 p.Ala262Thr missense_variant 0.33
mmpL5 778035 p.Val149Asp missense_variant 0.18
mmpR5 778271 c.-719C>T upstream_gene_variant 0.4
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
mmpS5 779630 c.-725T>C upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801138 p.Ser110Arg missense_variant 0.22
rplC 801159 c.351C>A synonymous_variant 0.29
fbiC 1303776 p.Lys282Asn missense_variant 0.67
fbiC 1303892 p.Ala321Glu missense_variant 0.17
fbiC 1303978 p.Gly350Arg missense_variant 0.17
fbiC 1305003 c.2073C>A synonymous_variant 0.5
Rv1258c 1406242 p.Ala367Ser missense_variant 0.13
Rv1258c 1406256 p.Leu362Trp missense_variant 0.12
Rv1258c 1406402 c.939C>A synonymous_variant 0.29
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407163 p.Leu60Val missense_variant 0.11
Rv1258c 1407200 c.141G>C synonymous_variant 0.12
embR 1416985 c.363G>T synonymous_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475714 n.2057G>T non_coding_transcript_exon_variant 1.0
fabG1 1673257 c.-183C>A upstream_gene_variant 0.18
fabG1 1673515 p.Gly26Trp missense_variant 0.67
fabG1 1673840 p.Arg134Leu missense_variant 0.33
inhA 1674643 p.Asp148Tyr missense_variant 0.33
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834480 c.939C>A synonymous_variant 0.33
rpsA 1834751 p.Leu404Phe missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101711 c.1332G>A synonymous_variant 0.22
ndh 2102275 c.768C>T synonymous_variant 0.25
ndh 2103016 c.27G>T synonymous_variant 0.67
katG 2154303 c.1809G>A synonymous_variant 0.4
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155216 p.Gly299Val missense_variant 0.4
katG 2156499 c.-388C>T upstream_gene_variant 0.25
PPE35 2167825 p.Gly930Cys missense_variant 0.5
PPE35 2169370 p.Gly415* stop_gained 0.29
PPE35 2169374 c.1239C>T synonymous_variant 0.29
PPE35 2170048 p.Leu189Val missense_variant 0.25
PPE35 2170053 p.Thr187Ser missense_variant 0.25
PPE35 2170282 p.Ala111Ser missense_variant 0.22
Rv1979c 2223112 p.Ser18Ile missense_variant 0.25
Rv1979c 2223123 c.42G>T synonymous_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289063 p.Gly60Val missense_variant 0.25
pncA 2289172 p.Gly24Cys missense_variant 0.4
kasA 2518047 c.-68G>T upstream_gene_variant 0.22
kasA 2518782 p.Pro223His missense_variant 0.2
eis 2715358 c.-26C>T upstream_gene_variant 0.25
eis 2715481 c.-149G>A upstream_gene_variant 0.22
ahpC 2726271 p.Asp27Tyr missense_variant 0.25
pepQ 2859718 p.Thr234Ile missense_variant 0.17
pepQ 2860537 c.-119C>A upstream_gene_variant 0.22
ribD 2986802 c.-37C>A upstream_gene_variant 0.4
Rv2752c 3064571 p.Val541Leu missense_variant 0.25
Rv2752c 3064682 p.Leu504Ile missense_variant 0.22
Rv2752c 3066233 c.-42G>A upstream_gene_variant 0.18
Rv2752c 3067039 c.-848T>C upstream_gene_variant 1.0
thyA 3073897 p.Ala192Asp missense_variant 0.5
ald 3086650 c.-170C>A upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087329 p.Asp170Glu missense_variant 0.25
ald 3087755 c.936G>T synonymous_variant 1.0
ald 3087824 c.1005G>A synonymous_variant 0.25
fbiD 3339262 p.Ala49Ser missense_variant 0.29
fbiD 3339664 p.Pro183Ala missense_variant 0.11
Rv3083 3449660 p.Trp386Leu missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475293 c.1287C>T synonymous_variant 0.25
whiB7 3568482 p.Trp66Cys missense_variant 0.25
Rv3236c 3612813 p.Thr102Ala missense_variant 0.75
fbiA 3640561 p.Ala7Ser missense_variant 0.33
fbiA 3641422 p.Asp294Tyr missense_variant 0.18
fbiA 3641518 p.Leu326Val missense_variant 0.2
alr 3840629 c.792C>T synonymous_variant 0.29
alr 3840822 p.Ala200Val missense_variant 0.15
rpoA 3877788 p.Glu240Asp missense_variant 0.33
rpoA 3878646 c.-139G>T upstream_gene_variant 0.67
clpC1 4039843 p.Glu288* stop_gained 0.29
clpC1 4039864 p.Asp281Tyr missense_variant 0.33
clpC1 4040395 p.Gly104Trp missense_variant 0.15
clpC1 4040417 c.288G>T synonymous_variant 0.2
panD 4044125 p.Ala53Ser missense_variant 0.33
embC 4240482 p.Pro207Gln missense_variant 0.15
embC 4241319 p.Pro486Gln missense_variant 0.15
embC 4241359 c.1497C>G synonymous_variant 0.18
embC 4241435 p.Ala525Pro missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242773 p.Leu971Met missense_variant 0.14
embA 4243455 p.Pro75Thr missense_variant 0.13
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244702 c.1470C>T synonymous_variant 0.29
embA 4244720 p.Tyr496* stop_gained 0.29
embA 4244795 c.1563G>T synonymous_variant 0.33
embA 4245253 p.Thr674Asn missense_variant 0.33
embA 4245606 p.Leu792Met missense_variant 0.17
embA 4246332 p.Gln1034Lys missense_variant 0.25
embB 4247536 c.1023C>A synonymous_variant 0.33
embB 4247899 p.Met462Ile missense_variant 0.14
aftB 4267547 c.1290C>A synonymous_variant 0.67
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268019 p.Ser273* stop_gained 0.5
aftB 4268032 p.Pro269Ser missense_variant 0.5
aftB 4268190 p.Ala216Asp missense_variant 0.25
ethA 4326133 c.1341C>A synonymous_variant 0.25
ethA 4326433 p.Gln347His missense_variant 0.67
ethA 4326720 p.Ala252Ser missense_variant 0.33
ethA 4328378 c.-905G>T upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407532 p.Ala224Val missense_variant 0.4
gid 4407563 p.Gly214Trp missense_variant 0.22
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407636 c.567G>T synonymous_variant 0.29
gid 4407927 p.Glu92Asp missense_variant 1.0