TB-Profiler result

Run: SRR11972264
Summary

Run ID: SRR11972264

Sample name:

Date: 03-04-2023 05:34:04

Number of reads: 430830

Percentage reads mapped: 95.13

Strain: lineage2.2.1.1

Drug-resistance: Pre-XDR-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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.97
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 7572 p.Ser91Pro missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764363 p.Gly332Arg missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289081 p.Pro54Leu missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 1.0 ethambutol
gid 4408100 c.102delG frameshift_variant 1.0 streptomycin
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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7558 p.Pro86Gln missense_variant 0.15
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9062 c.1761C>T synonymous_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491660 p.Ala293Val missense_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576160 c.813C>A synonymous_variant 0.12
ccsA 620504 p.Glu205Val missense_variant 0.22
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761017 p.Glu404Gly missense_variant 0.12
rpoB 761925 p.Met707Val missense_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763536 p.Arg56Leu missense_variant 0.12
rpoC 764615 p.Asn416Tyr missense_variant 0.22
rpoC 764742 p.Lys458Thr missense_variant 0.18
rpoC 764843 p.Ala492Thr missense_variant 0.18
rpoC 765024 p.Gln552Arg missense_variant 0.11
rpoC 765899 c.2530C>T synonymous_variant 0.15
rpoC 766335 p.Val989Ala missense_variant 0.15
rpoC 766379 p.Gly1004Ser missense_variant 0.13
rpoC 766723 c.3354G>A synonymous_variant 0.29
rpoC 766906 c.3537G>A synonymous_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777423 p.Leu353Pro missense_variant 0.12
mmpL5 778205 p.Met92Ile missense_variant 0.2
mmpL5 778428 p.His18Arg missense_variant 0.12
mmpS5 779553 c.-648A>G upstream_gene_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801098 p.Val97Ala missense_variant 0.11
fbiC 1303152 c.222C>A synonymous_variant 0.13
fbiC 1303516 p.Met196Val missense_variant 0.12
fbiC 1304348 p.Trp473Leu missense_variant 0.25
fbiC 1304669 p.Ser580* stop_gained 0.18
fbiC 1304853 c.1923C>G synonymous_variant 0.12
Rv1258c 1406673 p.Arg223Leu missense_variant 0.15
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416564 p.Ala262Thr missense_variant 0.12
embR 1417242 p.Arg36Trp missense_variant 0.13
atpE 1461168 p.Gln42* stop_gained 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.15
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.21
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.15
rrs 1472544 n.699C>G non_coding_transcript_exon_variant 0.12
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.12
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.16
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.24
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.24
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.19
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.33
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.24
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.18
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.18
rrs 1472659 n.814G>A non_coding_transcript_exon_variant 0.17
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.17
rrs 1472669 n.824_825insTAG non_coding_transcript_exon_variant 0.22
rrs 1472679 n.834_835insAC non_coding_transcript_exon_variant 0.17
rrs 1472684 n.841_846delGATCCG non_coding_transcript_exon_variant 0.17
rrs 1472697 n.852T>A non_coding_transcript_exon_variant 0.19
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.19
rrs 1472705 n.860G>A non_coding_transcript_exon_variant 0.2
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.18
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.18
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.18
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.17
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.16
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.16
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.24
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.24
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.24
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.12
rrs 1472953 n.1108_1109insA non_coding_transcript_exon_variant 0.15
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.15
rrs 1472958 n.1114delT non_coding_transcript_exon_variant 0.15
rrs 1472977 n.1132G>T non_coding_transcript_exon_variant 0.15
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.15
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.15
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.15
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.16
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.16
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.15
rrs 1473121 n.1276_1277insA non_coding_transcript_exon_variant 0.17
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.19
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.15
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.17
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.18
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.17
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.19
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.24
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.28
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.12
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.12
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.1
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.11
rrl 1476269 n.2612C>G non_coding_transcript_exon_variant 0.11
rrl 1476274 n.2617G>C non_coding_transcript_exon_variant 0.11
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.14
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.13
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.13
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.13
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.13
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.13
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.13
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.12
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.13
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.13
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.13
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.19
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.21
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.22
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.16
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.15
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.14
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.14
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.18
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.31
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.31
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.37
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.28
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.12
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.17
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.13
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.12
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.12
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.13
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.13
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.13
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.13
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.12
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.14
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.19
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.1
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.11
inhA 1674198 c.-4G>A upstream_gene_variant 0.17
rpsA 1834032 p.Tyr164Phe missense_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834720 c.1179C>A synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918405 p.Ser156Thr missense_variant 0.15
ndh 2102313 p.Gln244Lys missense_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156240 c.-129A>G upstream_gene_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168114 c.2499T>C synonymous_variant 0.12
PPE35 2169675 p.Asn313Ile missense_variant 0.15
PPE35 2170385 c.228G>T synonymous_variant 0.15
PPE35 2170392 p.Gly74Ala missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517939 c.-176G>A upstream_gene_variant 0.15
kasA 2518438 c.324C>T synonymous_variant 0.13
eis 2714426 p.Ala303Ser missense_variant 0.12
eis 2714846 p.Val163Ile missense_variant 1.0
ahpC 2726739 p.Pro183Ser missense_variant 0.18
pepQ 2860590 c.-172C>T upstream_gene_variant 0.12
ribD 2987344 p.Asp169Val missense_variant 0.13
Rv2752c 3064550 p.Gln548* stop_gained 0.13
Rv2752c 3065231 p.Gly321Trp missense_variant 0.2
thyX 3067544 p.Glu134Asp missense_variant 0.18
thyX 3068021 c.-76C>T upstream_gene_variant 0.12
thyA 3074252 p.Glu74Lys missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448939 p.Asp146Tyr missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474542 p.Ala179Val missense_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612979 c.137delG frameshift_variant 0.12
Rv3236c 3613075 c.42G>T synonymous_variant 0.17
alr 3841546 c.-126C>A upstream_gene_variant 0.16
rpoA 3878025 c.483C>T synonymous_variant 0.14
clpC1 4039813 p.Ala298Thr missense_variant 0.12
panD 4043866 p.Gly139Glu missense_variant 0.14
embC 4239711 c.-152C>A upstream_gene_variant 0.18
embC 4240078 c.216A>G synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242974 c.-259C>T upstream_gene_variant 0.13
embA 4243232 c.-1C>T upstream_gene_variant 0.15
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244265 p.Arg345Trp missense_variant 0.14
embA 4245149 c.1917C>A synonymous_variant 0.17
embB 4246555 c.42G>A synonymous_variant 0.29
embB 4246943 p.Gln144* stop_gained 0.13
embB 4247380 c.867C>T synonymous_variant 0.11
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4248705 p.Pro731Leu missense_variant 0.2
aftB 4267556 c.1281G>T synonymous_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267743 p.Arg365Leu missense_variant 0.18
aftB 4268293 p.Ser182Gly missense_variant 0.11
aftB 4269246 c.-410G>A upstream_gene_variant 0.18
ethA 4326085 c.1389T>C synonymous_variant 0.15
ethR 4326610 c.-939G>T upstream_gene_variant 0.15
ethA 4326794 p.Arg227His missense_variant 0.29
ethA 4327115 p.Ile120Thr missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407724 p.Leu160Pro missense_variant 0.11
gid 4407927 p.Glu92Asp missense_variant 1.0