TB-Profiler result

Run: SRR11972242
Summary

Run ID: SRR11972242

Sample name:

Date: 03-04-2023 05:33:16

Number of reads: 301913

Percentage reads mapped: 99.0

Strain: lineage2.2.1

Drug-resistance: Other

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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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
gyrA 7510 p.His70Arg missense_variant 0.25 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
tlyA 1918388 p.Leu150Pro missense_variant 0.18 capreomycin
pncA 2288662 c.539_*18delTCGAGTTGGTTTGCAGCTCCTGATGGCACCGCCGAACCGGG frameshift_variant&stop_lost&splice_region_variant 0.8 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 6208 c.969G>A synonymous_variant 0.13
gyrB 6953 p.Lys572Glu missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7696 p.Ala132Val missense_variant 0.2
gyrA 8632 p.Ala444Val missense_variant 0.22
gyrA 8896 p.Asp532Val missense_variant 0.18
gyrA 9235 p.Ser645Leu missense_variant 0.4
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9562 p.Met754Thr missense_variant 0.14
fgd1 490667 c.-116C>T upstream_gene_variant 0.15
fgd1 490880 p.Asp33Gly missense_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575465 p.Ala40Thr missense_variant 0.29
mshA 576288 p.Arg314Leu missense_variant 0.14
ccsA 620625 p.Ile245Met missense_variant 0.17
rpoB 760658 p.Glu284Asp missense_variant 0.25
rpoB 762367 p.Glu854Gly missense_variant 0.14
rpoB 762393 p.Val863Met missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763528 c.159G>T synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.43
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781889 c.330C>A synonymous_variant 0.4
fbiC 1302752 c.-179G>A upstream_gene_variant 0.14
fbiC 1302928 c.-3A>G upstream_gene_variant 0.12
fbiC 1303136 p.Gly69Val missense_variant 0.25
fbiC 1305371 p.Glu814Val missense_variant 0.14
fbiC 1305494 p.Ala855Glu missense_variant 0.15
Rv1258c 1406533 p.Gly270Arg missense_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407459 c.-119T>C upstream_gene_variant 0.22
embR 1416723 c.624delG frameshift_variant 0.22
embR 1416767 p.Leu194Pro missense_variant 0.25
atpE 1461133 p.Val30Asp missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473063 n.1218C>T non_coding_transcript_exon_variant 0.13
rrl 1473543 n.-115C>G upstream_gene_variant 0.11
rrl 1474152 n.495G>A non_coding_transcript_exon_variant 0.13
rrl 1476116 n.2461_2462delGG non_coding_transcript_exon_variant 0.12
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.15
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.17
rrl 1476269 n.2612C>G non_coding_transcript_exon_variant 0.18
rrl 1476274 n.2617G>C non_coding_transcript_exon_variant 0.18
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.18
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.2
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.2
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.2
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.2
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.2
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.2
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.19
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.19
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.19
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.19
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.14
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.16
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.16
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.17
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.16
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.12
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.12
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.29
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.24
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.19
fabG1 1673262 c.-178G>C upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.12
fabG1 1674091 p.Ala218Thr missense_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834417 c.876G>A synonymous_variant 0.25
rpsA 1834488 p.Gly316Asp missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918640 p.Ser234Leu missense_variant 0.14
ndh 2101832 p.Leu404Pro missense_variant 0.17
ndh 2102343 p.Ala234Thr missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156112 c.-1T>C upstream_gene_variant 0.92
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168258 c.2355G>C synonymous_variant 0.12
PPE35 2169290 c.1323C>T synonymous_variant 0.18
PPE35 2169554 c.1059C>T synonymous_variant 0.18
Rv1979c 2221883 c.1282C>T synonymous_variant 0.12
Rv1979c 2222065 p.Leu367Pro missense_variant 0.12
Rv1979c 2222202 c.963C>T synonymous_variant 0.15
Rv1979c 2223157 p.Gly3Asp missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288949 p.Ala98Val missense_variant 0.15
kasA 2518013 c.-102G>A upstream_gene_variant 0.18
kasA 2518130 p.Thr6Ser missense_variant 0.17
eis 2714786 p.Arg183Cys missense_variant 0.12
eis 2714846 p.Val163Ile missense_variant 0.23
eis 2715269 p.Ala22Thr missense_variant 0.18
eis 2715305 p.Glu10Lys missense_variant 0.13
ahpC 2725915 c.-278C>T upstream_gene_variant 0.13
ahpC 2726150 c.-43G>C upstream_gene_variant 0.12
ahpC 2726338 p.Val49Glu missense_variant 0.12
ribD 2987026 p.Ala63Val missense_variant 0.2
ribD 2987311 p.Gly158Asp missense_variant 0.33
thyX 3068013 c.-68C>T upstream_gene_variant 0.12
thyA 3073917 c.555C>T synonymous_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339457 p.Gln114* stop_gained 0.17
Rv3083 3449590 p.Ala363Thr missense_variant 0.2
Rv3083 3449985 c.1482G>A synonymous_variant 0.15
fprA 3473817 c.-190G>T upstream_gene_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474050 p.Ala15Val missense_variant 0.25
fprA 3474604 p.Arg200* stop_gained 0.4
fbiB 3640879 c.-656C>T upstream_gene_variant 0.7
fbiB 3640980 c.-555C>G upstream_gene_variant 0.2
fbiB 3642208 p.Asp225Gly missense_variant 0.29
alr 3840418 p.Cys335Arg missense_variant 0.17
rpoA 3877585 p.Leu308Pro missense_variant 0.12
clpC1 4038546 p.His720Arg missense_variant 0.2
clpC1 4039266 p.Asp480Ala missense_variant 0.12
clpC1 4039714 p.Tyr331His missense_variant 0.33
clpC1 4039730 c.975C>G synonymous_variant 0.25
clpC1 4040710 c.-6C>T upstream_gene_variant 0.17
panD 4044301 c.-20G>T upstream_gene_variant 0.15
embC 4240813 c.951C>T synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243904 c.672G>T synonymous_variant 0.14
embB 4246643 p.Thr44Pro missense_variant 0.2
embB 4246707 p.Gly65Val missense_variant 0.22
embB 4246972 c.459C>T synonymous_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268230 p.Ala203Thr missense_variant 0.25
ethA 4326474 p.Pro334Ala missense_variant 1.0
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
gid 4407994 c.208delA frameshift_variant 1.0