TB-Profiler result

Run: ERR2660542

Summary

Run ID: ERR2660542

Sample name:

Date: 31-03-2023 22:55:06

Number of reads: 1049418

Percentage reads mapped: 86.66

Strain: lineage4.3.2.1;lineage2.2.1

Drug-resistance: Sensitive


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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 0.79
lineage4 Euro-American LAM;T;S;X;H None 0.19
lineage4.3 Euro-American (LAM) mainly-LAM None 0.2
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.8
lineage4.3.2 Euro-American (LAM) LAM3 None 0.2
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.77
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 0.16
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
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 5520 p.Pro94Leu missense_variant 0.22
gyrA 7222 c.-80C>T upstream_gene_variant 0.19
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 491742 c.960T>C synonymous_variant 0.87
mshA 575907 p.Ala187Val missense_variant 0.76
ccsA 620625 p.Ile245Met missense_variant 0.78
rpoC 763031 c.-339T>C upstream_gene_variant 0.88
rpoC 764995 c.1626C>G synonymous_variant 0.27
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.88
mmpL5 776182 p.Asp767Asn missense_variant 0.92
mmpS5 779615 c.-710C>G upstream_gene_variant 0.84
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.75
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.13
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.33
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.33
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.29
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.29
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.5
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.5
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.71
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.62
rrs 1472659 n.814G>A non_coding_transcript_exon_variant 0.62
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.62
rrs 1472669 n.824_825insTAG non_coding_transcript_exon_variant 0.62
rrs 1472677 n.832C>G non_coding_transcript_exon_variant 0.62
rrs 1472678 n.833T>A non_coding_transcript_exon_variant 0.62
rrs 1472679 n.834_835insAC non_coding_transcript_exon_variant 0.62
rrs 1472684 n.841_846delGATCCG non_coding_transcript_exon_variant 0.56
rrs 1472697 n.852T>A non_coding_transcript_exon_variant 0.56
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.62
rrs 1472705 n.860G>A non_coding_transcript_exon_variant 0.62
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.7
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.7
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.7
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.7
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.7
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.7
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.54
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.54
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.54
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.45
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.45
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.29
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.22
rrs 1472953 n.1108_1109insA non_coding_transcript_exon_variant 0.22
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.2
rrs 1472958 n.1114delT non_coding_transcript_exon_variant 0.2
rrs 1472977 n.1132G>T non_coding_transcript_exon_variant 0.22
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.22
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.33
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.33
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.38
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.38
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.38
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.43
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.43
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.29
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.33
rrs 1473070 n.1225G>A non_coding_transcript_exon_variant 0.33
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.18
rrs 1473179 n.1334C>T non_coding_transcript_exon_variant 0.18
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.17
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.17
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.17
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 1.0
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.67
rrl 1475201 n.1544G>A non_coding_transcript_exon_variant 0.67
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.67
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.67
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.67
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.22
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.25
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.24
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.26
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.26
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.26
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.28
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.26
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.26
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.28
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.28
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.28
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.3
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.32
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.24
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.2
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.18
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.17
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.18
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.26
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.33
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.33
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.38
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.43
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.41
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.36
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.35
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.35
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.37
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.37
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.37
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.37
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.41
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.44
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.44
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.44
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.44
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.47
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.5
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.5
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.56
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.5
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.5
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.36
rrl 1476621 n.2964C>A non_coding_transcript_exon_variant 0.36
rrl 1476624 n.2967T>A non_coding_transcript_exon_variant 0.36
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.46
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.38
rrl 1476637 n.2980C>G non_coding_transcript_exon_variant 0.42
rpsA 1834177 c.636A>C synonymous_variant 0.84
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.88
PPE35 2167926 p.Leu896Ser missense_variant 0.91
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.26
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339117 c.-1C>A upstream_gene_variant 0.72
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.76
fbiA 3641332 p.Gly264Arg missense_variant 0.9
clpC1 4038287 c.2418C>T synonymous_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.91
embB 4249640 c.3127T>C synonymous_variant 0.72
aftB 4267647 p.Asp397Gly missense_variant 0.69
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.8
gid 4407927 p.Glu92Asp missense_variant 0.88
gid 4408156 p.Leu16Arg missense_variant 0.22