TB-Profiler result

Run: SRR11972212
Summary

Run ID: SRR11972212

Sample name:

Date: 03-04-2023 05:32:09

Number of reads: 360336

Percentage reads mapped: 50.01

Strain: lineage2.2.1.1

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
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 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
rpoC 764841 p.Ile491Thr missense_variant 0.2 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.67 isoniazid
thyX 3067961 c.-16C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
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 5392 c.153C>T synonymous_variant 0.33
gyrB 6076 c.837C>T synonymous_variant 0.2
gyrB 6950 p.Leu571Val missense_variant 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491129 p.Thr116Ser missense_variant 0.25
fgd1 491226 c.444C>T synonymous_variant 0.33
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576211 c.864C>A synonymous_variant 0.22
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762320 c.2514C>A synonymous_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764881 c.1512G>A synonymous_variant 0.2
rpoC 764916 p.Leu516Pro missense_variant 0.3
rpoC 766519 c.3152delG frameshift_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 1.0
mmpL5 776815 p.Gln556* stop_gained 0.12
mmpL5 777266 c.1215G>A synonymous_variant 0.17
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781854 p.Arg99Cys missense_variant 0.4
rplC 801441 c.633G>A synonymous_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416545 c.802delA frameshift_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472119 n.274G>A non_coding_transcript_exon_variant 0.18
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.17
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.18
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.18
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.18
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.22
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.2
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.2
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.2
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.2
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.2
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.2
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.2
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.2
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.2
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.4
rrs 1472932 n.1087C>A non_coding_transcript_exon_variant 0.13
rrs 1472952 n.1107_1108insAG non_coding_transcript_exon_variant 0.6
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.47
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.47
rrs 1472977 n.1132G>T non_coding_transcript_exon_variant 0.47
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.5
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.5
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.5
rrs 1472992 n.1147A>C non_coding_transcript_exon_variant 0.5
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.56
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.56
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.56
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.56
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.65
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.6
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.59
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.69
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.64
rrs 1473070 n.1225G>A non_coding_transcript_exon_variant 0.6
rrs 1473089 n.1244A>C non_coding_transcript_exon_variant 0.53
rrs 1473093 n.1248C>A non_coding_transcript_exon_variant 0.53
rrs 1473094 n.1249T>A non_coding_transcript_exon_variant 0.53
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.53
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.53
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.53
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.53
rrs 1473120 n.1275C>T non_coding_transcript_exon_variant 0.6
rrs 1473124 n.1279A>G non_coding_transcript_exon_variant 0.6
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.58
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.53
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.53
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.53
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.53
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.53
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.53
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.53
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.53
rrs 1473179 n.1334C>T non_coding_transcript_exon_variant 0.53
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.53
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.47
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.4
rrl 1473985 n.328A>G non_coding_transcript_exon_variant 0.5
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.33
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.33
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.33
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.27
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.27
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.27
rrl 1475687 n.2030C>T non_coding_transcript_exon_variant 0.18
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.18
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.18
rrl 1475707 n.2050T>A non_coding_transcript_exon_variant 0.18
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.22
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.2
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.29
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.22
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.22
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.22
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.22
rrl 1475843 n.2186G>A non_coding_transcript_exon_variant 0.33
rrl 1475849 n.2192G>A non_coding_transcript_exon_variant 0.33
rrl 1475853 n.2196C>T non_coding_transcript_exon_variant 0.33
rrl 1476126 n.2469C>T non_coding_transcript_exon_variant 0.29
rrl 1476128 n.2471T>A non_coding_transcript_exon_variant 0.38
rrl 1476135 n.2478T>C non_coding_transcript_exon_variant 0.38
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.38
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.38
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.43
rrl 1476165 n.2508T>C non_coding_transcript_exon_variant 0.43
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.25
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.22
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.25
rrl 1476251 n.2594T>A non_coding_transcript_exon_variant 0.38
rrl 1476252 n.2595T>A non_coding_transcript_exon_variant 0.38
rrl 1476256 n.2599A>C non_coding_transcript_exon_variant 0.38
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.43
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.43
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.3
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.33
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.3
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.3
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.3
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.3
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.3
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.3
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.3
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.3
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.5
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.5
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.62
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.67
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.47
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.6
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.6
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.77
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.15
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.67
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.62
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.14
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.13
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.13
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.87
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.13
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.87
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 1.0
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 1.0
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 1.0
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 1.0
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 1.0
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 1.0
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 1.0
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 1.0
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 1.0
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 1.0
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 1.0
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 1.0
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 1.0
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 1.0
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 1.0
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 1.0
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 1.0
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 1.0
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 1.0
rrl 1476607 n.2950C>T non_coding_transcript_exon_variant 1.0
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 1.0
rrl 1476621 n.2964C>A non_coding_transcript_exon_variant 1.0
rrl 1476624 n.2967T>A non_coding_transcript_exon_variant 1.0
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 1.0
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 1.0
rrl 1476637 n.2980C>G non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.5
inhA 1674306 c.105G>A synonymous_variant 0.67
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102816 p.Leu76Pro missense_variant 0.12
ndh 2103172 c.-130C>T upstream_gene_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156180 c.-70delT upstream_gene_variant 0.33
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168615 c.1998A>G synonymous_variant 0.13
PPE35 2168862 p.Leu584Arg missense_variant 0.12
Rv1979c 2222441 p.Ala242Thr missense_variant 0.15
Rv1979c 2222494 c.670delG frameshift_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714555 p.Asp260Asn missense_variant 0.14
eis 2714846 p.Val163Ile missense_variant 1.0
thyA 3074232 p.Trp80* stop_gained 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448631 p.Gly43Asp missense_variant 0.12
Rv3083 3448791 p.Glu96Asp missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474329 p.Ser108Tyr missense_variant 1.0
Rv3236c 3612692 p.Arg142Leu missense_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612978 p.Gly47Ser missense_variant 0.11
Rv3236c 3613200 c.-84T>C upstream_gene_variant 0.12
Rv3236c 3613267 c.-151G>C upstream_gene_variant 0.12
fbiB 3640614 c.-921C>T upstream_gene_variant 0.13
fbiA 3641069 p.Tyr176Ser missense_variant 0.2
fbiB 3642249 p.Asp239Asn missense_variant 0.29
clpC1 4038747 p.Arg653His missense_variant 0.12
clpC1 4039099 p.Arg536Gly missense_variant 0.13
clpC1 4040335 c.370C>T synonymous_variant 0.18
embC 4240972 c.1110C>T synonymous_variant 0.29
embC 4241936 c.2074A>C synonymous_variant 0.15
embC 4242017 c.2156delA frameshift_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244679 p.Ala483Thr missense_variant 0.15
embB 4246005 c.-509C>T upstream_gene_variant 0.15
embA 4246085 p.Glu951Asp missense_variant 0.14
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4246563 p.Leu17Trp missense_variant 0.5
embB 4246567 c.54G>T synonymous_variant 0.5
embB 4247001 p.Gly163Glu missense_variant 0.33
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4248845 p.Gly778Cys missense_variant 0.33
embB 4249611 p.Asn1033Ser missense_variant 0.33
aftB 4266974 c.1863C>T synonymous_variant 0.5
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338353 p.Pro57Ser missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338654 c.-133A>T upstream_gene_variant 0.12
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0