TB-Profiler result

Run: SRR13423629
Summary

Run ID: SRR13423629

Sample name:

Date: 03-04-2023 08:54:33

Number of reads: 1618033

Percentage reads mapped: 48.88

Strain: lineage2.2.1

Drug-resistance: MDR-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
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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.8 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288750 c.491_492insA frameshift_variant 0.27 pyrazinamide
pncA 2288757 p.Gly162Asp missense_variant 0.17 pyrazinamide
pncA 2288954 c.287delA frameshift_variant 0.76 pyrazinamide, pyrazinamide
embB 4248003 p.Gln497Arg 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
gyrB 5119 c.-121T>C upstream_gene_variant 1.0
gyrB 5545 c.306A>G synonymous_variant 0.13
gyrB 5711 p.Leu158Phe missense_variant 0.12
gyrB 5753 c.516delG frameshift_variant 0.15
gyrA 6928 c.-374G>A upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7852 p.Gly184Asp missense_variant 0.12
gyrA 8201 c.900C>A synonymous_variant 0.22
gyrA 8320 p.Ser340Ile missense_variant 0.22
gyrA 8357 c.1056G>A synonymous_variant 0.14
gyrA 8754 c.1456delA frameshift_variant 0.11
gyrA 8924 c.1623C>T synonymous_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9639 p.Gly780Arg missense_variant 0.17
fgd1 490960 p.Ala60Thr missense_variant 0.11
fgd1 491257 p.Gly159Cys missense_variant 0.12
fgd1 491637 c.855C>A synonymous_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759914 c.108T>A synonymous_variant 0.11
rpoB 760480 p.Arg225Leu missense_variant 0.13
rpoB 761020 p.Ala405Val missense_variant 0.12
rpoB 761418 p.Ala538Ser missense_variant 0.85
rpoC 762785 c.-585C>T upstream_gene_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763359 c.-11A>G upstream_gene_variant 0.22
rpoC 764040 p.Ser224Ile missense_variant 0.14
rpoC 764143 c.774G>T synonymous_variant 0.11
rpoC 765358 p.Met663Ile missense_variant 0.13
rpoC 766202 p.Gly945Ser missense_variant 1.0
rpoC 766860 p.Arg1164Gln missense_variant 0.14
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 776986 c.1493_1494delCG frameshift_variant 0.18
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781930 p.Gly124Asp missense_variant 0.12
rplC 801392 c.587delG frameshift_variant 0.18
fbiC 1303002 c.76_80delTTGCG frameshift_variant 0.11
fbiC 1303395 p.Trp155* stop_gained 0.13
fbiC 1305347 p.Asp806Gly missense_variant 0.12
fbiC 1305390 c.2462delG frameshift_variant 0.12
Rv1258c 1406253 p.Gly363Val missense_variant 0.97
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416593 p.Glu252Gly missense_variant 0.12
embR 1416676 c.672G>A synonymous_variant 0.12
embR 1416859 c.489C>A synonymous_variant 0.17
atpE 1460897 c.-147delT upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.11
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.1
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.43
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.45
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.45
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.55
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.55
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.53
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.53
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.39
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.15
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.37
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.51
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.43
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.12
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.51
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.55
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.55
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.56
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.68
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.75
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.75
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.75
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.63
rrs 1472669 n.824_825insTGGA non_coding_transcript_exon_variant 0.71
rrs 1472678 n.833T>G non_coding_transcript_exon_variant 0.67
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.67
rrs 1472682 n.839_843delGGGAT non_coding_transcript_exon_variant 0.7
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.72
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.7
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.74
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.68
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.81
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.8
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.78
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.78
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.62
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.27
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.17
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.17
rrs 1473317 n.1474_1475dupCG non_coding_transcript_exon_variant 0.12
rrl 1474747 n.1090C>A non_coding_transcript_exon_variant 0.16
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.26
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.33
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.33
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.33
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.33
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.33
rrl 1474797 n.1140G>A non_coding_transcript_exon_variant 0.33
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.33
rrl 1474799 n.1142G>A non_coding_transcript_exon_variant 0.33
rrl 1474801 n.1144G>C non_coding_transcript_exon_variant 0.33
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.35
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.31
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.35
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.36
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.36
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.36
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 0.42
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.48
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.48
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.45
rrl 1474869 n.1212G>C non_coding_transcript_exon_variant 0.45
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.36
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.26
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.22
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 0.18
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.18
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.17
rrl 1474920 n.1263G>A non_coding_transcript_exon_variant 0.15
rrl 1475174 n.1520delG non_coding_transcript_exon_variant 0.12
rrl 1475541 n.1884G>T non_coding_transcript_exon_variant 0.12
rrl 1475626 n.1972delG non_coding_transcript_exon_variant 0.12
rrl 1475707 n.2050T>C non_coding_transcript_exon_variant 0.38
rrl 1475713 n.2056C>G non_coding_transcript_exon_variant 0.39
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.41
rrl 1475751 n.2094C>G non_coding_transcript_exon_variant 0.41
rrl 1475752 n.2095C>A non_coding_transcript_exon_variant 0.41
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.41
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.47
rrl 1475776 n.2119G>T non_coding_transcript_exon_variant 0.48
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.48
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.45
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.47
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.47
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.44
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.44
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.33
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.21
rrl 1476071 n.2414C>A non_coding_transcript_exon_variant 0.25
rrl 1476130 n.2473G>A non_coding_transcript_exon_variant 0.4
rrl 1476135 n.2478T>C non_coding_transcript_exon_variant 0.45
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.74
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.85
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.12
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.19
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.85
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.84
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.84
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.84
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.84
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.84
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.84
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.84
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.84
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.76
rrl 1476214 n.2557G>C non_coding_transcript_exon_variant 0.56
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.85
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.89
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.17
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.85
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.16
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.82
rrl 1476252 n.2595T>A non_coding_transcript_exon_variant 0.67
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.14
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.85
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.88
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.8
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.8
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.8
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.8
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.77
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.8
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.78
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.79
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.79
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.8
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.84
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.85
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.84
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.86
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.83
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.83
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.85
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.85
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.59
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.77
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.82
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.82
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.61
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.78
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.7
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.62
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.57
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.53
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.54
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.55
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.45
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.47
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.47
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.45
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.45
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.29
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.25
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.24
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.25
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.14
inhA 1674210 c.9A>C synonymous_variant 0.87
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918042 p.Asp35Tyr missense_variant 0.14
ndh 2101727 p.Arg439Leu missense_variant 0.29
ndh 2101890 c.1152delC frameshift_variant 0.14
ndh 2102243 p.Arg267Gln missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155965 p.His49Gln missense_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168022 p.Leu864Pro missense_variant 0.11
PPE35 2170031 c.581delG frameshift_variant 0.12
PPE35 2170638 c.-26A>G upstream_gene_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518526 c.416delC frameshift_variant 0.2
kasA 2518615 c.504_505dupGT frameshift_variant 0.12
folC 2747776 c.-178G>A upstream_gene_variant 0.12
pepQ 2859756 c.663C>T synonymous_variant 0.12
pepQ 2859855 c.564G>A synonymous_variant 0.18
pepQ 2860423 c.-5G>C upstream_gene_variant 0.1
ribD 2987398 c.563_564delGC frameshift_variant 0.15
Rv2752c 3064527 c.1665C>A synonymous_variant 0.29
Rv2752c 3064883 p.Ser437Gly missense_variant 0.14
Rv2752c 3065362 p.Gly277Asp missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087185 c.367delG frameshift_variant 0.1
ald 3087926 c.1107G>A synonymous_variant 0.13
fbiD 3339377 p.Asp87Gly missense_variant 0.11
fbiD 3339385 p.Asp90Tyr missense_variant 0.16
Rv3083 3448728 c.225C>A synonymous_variant 0.12
Rv3083 3449226 p.Glu241Asp missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474451 p.Arg149Trp missense_variant 0.2
fprA 3474586 c.581delT frameshift_variant 0.13
fprA 3474620 p.Ala205Asp missense_variant 0.15
whiB7 3568746 c.-70_-68delACC upstream_gene_variant 0.11
Rv3236c 3612013 p.Ile368Met missense_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640763 p.Asp74Gly missense_variant 0.11
fbiA 3640849 p.Glu103* stop_gained 0.14
fbiB 3641274 c.-261G>A upstream_gene_variant 0.12
fbiB 3642132 p.Ala200Thr missense_variant 0.15
rpoA 3877969 p.Ala180Val missense_variant 1.0
rpoA 3878389 p.Arg40His missense_variant 0.17
rpoA 3878614 c.-108_-107insC upstream_gene_variant 0.2
panD 4044313 c.-32C>T upstream_gene_variant 0.2
embC 4240047 p.Pro62Leu missense_variant 0.11
embC 4242251 p.Asp797Tyr missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242680 p.Ala940Thr missense_variant 0.17
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243550 p.Phe106Leu missense_variant 0.12
embA 4243965 p.Arg245Trp missense_variant 0.12
embA 4245583 p.Asp784Gly missense_variant 0.12
embB 4246130 c.-384T>C upstream_gene_variant 0.17
embB 4246559 c.50delT frameshift_variant 0.17
embB 4247334 p.Arg274His missense_variant 0.15
embB 4247894 p.Pro461Ala missense_variant 1.0
embB 4249377 p.Leu955Pro missense_variant 0.1
aftB 4267279 p.Arg520Trp missense_variant 0.29
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268088 c.748delT frameshift_variant 0.18
aftB 4269533 c.-697C>T upstream_gene_variant 0.18
ubiA 4269733 p.Ala34Val missense_variant 0.12
ethA 4326486 p.Gly330Ser missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338644 c.-123C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0