TB-Profiler result

Run: SRR6397548
Summary

Run ID: SRR6397548

Sample name:

Date: 04-04-2023 14:01:54

Number of reads: 2003642

Percentage reads mapped: 27.12

Strain: lineage1.2.1.2.1

Drug-resistance: HR-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
lineage1 Indo-Oceanic EAI RD239 0.99
lineage1.2.1 Indo-Oceanic EAI2 RD239 0.99
lineage1.2.1.2 Indo-Oceanic NA RD239 0.99
lineage1.2.1.2.1 Indo-Oceanic NA RD239 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.5 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 0.97
rpoC 763884 p.Ala172Val missense_variant 0.98
rpoC 763886 c.517C>A synonymous_variant 0.98
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.98
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.18
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.24
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.27
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.28
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.4
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.44
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.44
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.44
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.45
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.47
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.46
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.44
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.44
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.44
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.43
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.35
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.33
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.32
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.22
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.16
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.19
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.25
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.53
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.58
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.58
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.58
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.59
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.59
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.59
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.59
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.58
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.59
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.59
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.59
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.6
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.6
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.15
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.19
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.46
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.47
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.49
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.49
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.5
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.5
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.47
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.47
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.15
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 1.0
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.14
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.13
rrl 1474824 n.1167A>C non_coding_transcript_exon_variant 0.13
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.13
rrl 1474830 n.1173A>C non_coding_transcript_exon_variant 0.13
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.14
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 0.15
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.15
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.16
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.16
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.16
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.16
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.15
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.15
rrl 1474903 n.1246T>A non_coding_transcript_exon_variant 0.15
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.15
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.15
rrl 1474920 n.1263G>C non_coding_transcript_exon_variant 0.14
rrl 1474928 n.1271C>A non_coding_transcript_exon_variant 0.14
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.37
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.51
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.65
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.67
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.67
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.67
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.67
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.68
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.68
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.68
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.69
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.69
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.7
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.7
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.71
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.73
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.73
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.73
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.85
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.86
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.86
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.86
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.86
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.87
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.87
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.9
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.88
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.88
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.87
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.83
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.81
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.71
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.58
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.54
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.54
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.53
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.55
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.54
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.53
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.53
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.54
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.54
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.55
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.53
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.47
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.47
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.4
rrl 1476595 n.2938C>G non_coding_transcript_exon_variant 0.14
rrl 1476596 n.2939C>T non_coding_transcript_exon_variant 0.13
inhA 1674162 c.-40C>T upstream_gene_variant 0.98
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.98
Rv1979c 2222308 p.Asp286Gly missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.98
kasA 2519048 p.Gly312Ser missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568488 c.191delG frameshift_variant 1.0
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240447 c.585G>A synonymous_variant 0.18
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246431 p.Asp1067Asn missense_variant 0.17
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
whiB6 4338361 p.Arg54Gln missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0