TB-Profiler result

Run: SRR11972449
Summary

Run ID: SRR11972449

Sample name:

Date: 03-04-2023 05:42:49

Number of reads: 1045409

Percentage reads mapped: 96.16

Strain: lineage2.2

Drug-resistance: MDR-TB

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.8 isoniazid
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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
gyrA 6439 c.-863C>T upstream_gene_variant 0.15
gyrB 6446 p.Ala403Ser missense_variant 0.17
gyrB 7097 p.Glu620* stop_gained 0.15
gyrB 7169 p.Ala644Thr missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8020 p.Thr240Ile missense_variant 0.22
gyrA 9518 p.Glu739Asp missense_variant 0.33
fgd1 490793 p.Leu4Pro missense_variant 0.2
fgd1 491379 c.597C>A synonymous_variant 0.4
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575789 p.Tyr148Asp missense_variant 0.22
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 0.95
rpoB 759843 p.Pro13Ser missense_variant 0.17
rpoB 761998 p.Leu731Pro missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764058 p.Ala230Val missense_variant 1.0
mmpL5 775632 p.Gln950Pro missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775964 c.2517G>C synonymous_variant 0.33
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777190 p.Tyr431His missense_variant 0.18
mmpL5 777757 p.Ala242Ser missense_variant 0.5
mmpR5 778379 c.-611C>T upstream_gene_variant 0.5
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781476 c.-84T>G upstream_gene_variant 0.29
rpsL 781847 p.Lys96Asn missense_variant 0.15
rplC 801014 p.Gln69Pro missense_variant 0.2
fbiC 1302845 c.-86T>C upstream_gene_variant 0.22
fbiC 1304256 c.1326G>A synonymous_variant 0.22
fbiC 1304451 c.1521C>T synonymous_variant 0.14
fbiC 1304883 p.Glu651Asp missense_variant 0.29
Rv1258c 1406504 c.837C>T synonymous_variant 0.17
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1417034 p.Ile105Thr missense_variant 0.11
atpE 1460884 c.-161C>G upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473592 n.-66C>T upstream_gene_variant 0.17
rrl 1474101 n.444C>A non_coding_transcript_exon_variant 0.12
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.18
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.22
rrl 1474174 n.517A>G non_coding_transcript_exon_variant 0.12
rrl 1474183 n.526T>C non_coding_transcript_exon_variant 0.12
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.12
rrl 1474186 n.529A>G non_coding_transcript_exon_variant 0.12
rrl 1474201 n.544T>C non_coding_transcript_exon_variant 0.13
rrl 1474202 n.545T>A non_coding_transcript_exon_variant 0.13
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.12
rrl 1475132 n.1475T>A non_coding_transcript_exon_variant 0.15
rrl 1475208 n.1551C>T non_coding_transcript_exon_variant 0.22
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.17
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.31
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.29
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.29
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.29
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.29
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.29
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.29
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.29
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.29
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.29
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.29
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.29
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.25
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.25
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.29
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.29
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.29
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.16
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.25
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.17
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.14
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.14
fabG1 1674023 p.Asp195Val missense_variant 0.25
inhA 1674751 p.Val184Leu missense_variant 0.29
rpsA 1833396 c.-145delG upstream_gene_variant 0.14
rpsA 1833736 c.195C>A synonymous_variant 0.25
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834553 p.Val338Phe missense_variant 0.22
rpsA 1834895 p.Ser452Arg missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155285 p.His276Arg missense_variant 0.25
katG 2156151 c.-40T>A upstream_gene_variant 0.22
PPE35 2167865 c.2748G>C synonymous_variant 0.33
PPE35 2167868 c.2745A>C synonymous_variant 0.33
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169127 p.Val496Ile missense_variant 0.33
PPE35 2169732 p.Asn294Ser missense_variant 0.13
Rv1979c 2222183 p.Thr328Ser missense_variant 0.22
Rv1979c 2222826 c.338delT frameshift_variant 0.2
Rv1979c 2223064 p.Leu34Pro missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289315 c.-74A>G upstream_gene_variant 0.11
kasA 2518147 c.33C>T synonymous_variant 0.33
ahpC 2726338 p.Val49Gly missense_variant 0.4
folC 2746538 p.His354Pro missense_variant 1.0
folC 2747437 p.Met54Ile missense_variant 0.67
folC 2747583 p.Ser6Pro missense_variant 0.33
Rv2752c 3064767 c.1425G>T synonymous_variant 0.25
Rv2752c 3064821 c.1371C>A synonymous_variant 0.33
Rv2752c 3064970 p.Lys408Glu missense_variant 1.0
thyX 3067216 p.Ser244Arg missense_variant 0.4
ald 3086654 c.-166T>A upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086806 c.-14C>T upstream_gene_variant 0.12
ald 3087513 p.Ala232Ser missense_variant 0.29
ald 3087737 c.918G>A synonymous_variant 0.12
Rv3083 3448485 c.-19C>T upstream_gene_variant 0.15
Rv3083 3449123 p.Val207Ala missense_variant 0.25
Rv3083 3449366 p.Pro288Leu missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474608 p.Gly201Val missense_variant 0.2
Rv3236c 3612501 p.Val206Ile missense_variant 0.2
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613229 c.-113G>T upstream_gene_variant 0.17
fbiA 3640990 p.Cys150Arg missense_variant 0.25
alr 3840284 p.Trp379* stop_gained 0.13
alr 3840683 c.738G>A synonymous_variant 0.5
alr 3841043 c.378C>T synonymous_variant 0.2
alr 3841523 c.-103G>T upstream_gene_variant 0.2
rpoA 3878644 c.-143_-138delCTCGGG upstream_gene_variant 0.15
panD 4044112 p.Thr57Asn missense_variant 0.17
embC 4239965 p.Val35Met missense_variant 0.11
embC 4240648 c.786C>T synonymous_variant 0.4
embC 4241958 p.Arg699Leu missense_variant 1.0
embA 4242337 c.-896C>A upstream_gene_variant 0.5
embC 4242612 p.Phe917Tyr missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242974 c.3113delT frameshift_variant 0.17
embA 4243096 c.-137A>T upstream_gene_variant 0.25
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244837 c.1605G>A synonymous_variant 0.29
embA 4245819 p.Ser863Gly missense_variant 0.67
embB 4247068 c.555T>C synonymous_variant 0.25
embB 4247090 p.Thr193Ala missense_variant 0.17
embB 4247098 c.585C>G synonymous_variant 0.18
embB 4249258 c.2745G>T synonymous_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 0.86
ubiA 4269626 p.Tyr70His missense_variant 0.17
ethA 4326082 c.1392C>T synonymous_variant 0.2
ethA 4326905 p.Leu190Pro missense_variant 0.22
ethA 4327328 p.Arg49Leu missense_variant 0.15
ethA 4327472 c.2T>G start_lost 1.0
ethR 4327645 p.Ala33Thr missense_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0