TB-Profiler result

Run: ERR212100
Summary

Run ID: ERR212100

Sample name:

Date: 31-03-2023 15:47:30

Number of reads: 5193835

Percentage reads mapped: 89.26

Strain: lineage4;lineage1.2.2.1

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
lineage4 Euro-American LAM;T;S;X;H None 0.13
lineage1 Indo-Oceanic EAI RD239 0.87
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.87
lineage1.2.2.1 Indo-Oceanic NA RD239 0.85
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 5075 c.-165C>T upstream_gene_variant 0.88
gyrB 6112 p.Met291Ile missense_variant 0.87
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.85
gyrA 9143 c.1842T>C synonymous_variant 0.81
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491060 p.Met93Thr missense_variant 0.83
fgd1 491742 c.960T>C synonymous_variant 0.89
ccsA 620659 p.Arg257Cys missense_variant 0.8
rpoC 763031 c.-339T>C upstream_gene_variant 0.89
rpoC 763884 p.Ala172Val missense_variant 0.86
rpoC 763886 c.517C>A synonymous_variant 0.86
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.91
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800899 p.Ala31Thr missense_variant 0.88
embR 1417019 p.Cys110Tyr missense_variant 0.85
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471842 n.-4T>G upstream_gene_variant 0.84
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.11
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.13
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.13
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.13
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.12
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.13
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.13
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.13
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.13
rrs 1472953 n.1108_1109insA non_coding_transcript_exon_variant 0.17
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.17
rrs 1472958 n.1114delT non_coding_transcript_exon_variant 0.17
rrs 1473124 n.1279A>T non_coding_transcript_exon_variant 0.14
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.16
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.17
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.16
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.17
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.18
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.18
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.18
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.18
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 0.16
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.13
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.13
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.14
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.18
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.19
rrl 1474800 n.1143T>C non_coding_transcript_exon_variant 0.18
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.18
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.25
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.27
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.28
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.28
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.23
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.2
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.16
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.13
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.13
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.12
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.12
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.12
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.12
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.12
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.12
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.12
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.13
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.29
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.3
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.31
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.33
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.38
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.4
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.41
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.53
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.53
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.53
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.39
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.31
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.14
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.16
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.15
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.15
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.15
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.15
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.15
rrl 1476607 n.2950C>T non_coding_transcript_exon_variant 0.15
rrl 1476608 n.2951C>A non_coding_transcript_exon_variant 0.15
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.15
rrl 1476621 n.2964C>A non_coding_transcript_exon_variant 0.14
rrl 1476624 n.2967T>G non_coding_transcript_exon_variant 0.14
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.14
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.14
rrl 1476637 n.2980C>G non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.9
katG 2156465 c.-354C>T upstream_gene_variant 0.77
PPE35 2167926 p.Leu896Ser missense_variant 0.91
PPE35 2169866 c.747G>C synonymous_variant 0.25
PPE35 2170070 c.543G>A synonymous_variant 0.8
Rv1979c 2222308 p.Asp286Gly missense_variant 0.86
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.87
eis 2714569 p.Ala255Gly missense_variant 0.19
ahpC 2726051 c.-142G>A upstream_gene_variant 0.89
folC 2747798 c.-200A>G upstream_gene_variant 0.86
pepQ 2859392 p.Val343Leu missense_variant 0.81
thyX 3068115 c.-170C>T upstream_gene_variant 0.9
thyA 3074034 c.438T>C synonymous_variant 0.89
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.86
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.85
fprA 3475159 p.Asn385Asp missense_variant 0.82
clpC1 4038857 c.1848C>A synonymous_variant 0.17
clpC1 4040517 p.Val63Ala missense_variant 0.85
embC 4239842 c.-21C>A upstream_gene_variant 0.19
embC 4240671 p.Thr270Ile missense_variant 0.89
embC 4240750 c.888C>T synonymous_variant 0.88
embC 4241042 p.Asn394Asp missense_variant 0.86
embC 4242425 p.Arg855Gly missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.12
embA 4245969 p.Pro913Ser missense_variant 0.82
embB 4247646 p.Glu378Ala missense_variant 0.86
aftB 4267051 p.Glu596Lys missense_variant 0.86
ubiA 4269387 p.Glu149Asp missense_variant 0.85
ubiA 4269529 p.Ala102Gly missense_variant 0.27
aftB 4269606 c.-770T>C upstream_gene_variant 0.84
ethA 4326439 p.Asn345Lys missense_variant 0.84
ethR 4327450 c.-99G>A upstream_gene_variant 0.81
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.86
gid 4407588 c.615A>G synonymous_variant 0.95
gid 4407873 c.330G>T synonymous_variant 0.84