TB-Profiler result

Run: SRR6153036
Summary

Run ID: SRR6153036

Sample name:

Date: 04-04-2023 13:06:59

Number of reads: 244281

Percentage reads mapped: 2.93

Strain:

Drug-resistance: Other

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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
lineage1.2.1 Indo-Oceanic EAI2 RD239 1.0
lineage1.2.1.2 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 0.98 streptomycin
embB 4247729 p.Gly406Ser missense_variant 1.0 ethambutol
gid 4408068 p.Trp45* stop_gained 1.0 streptomycin
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 6928 c.-374G>A upstream_gene_variant 0.22
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 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9329 c.2028C>A synonymous_variant 1.0
fgd1 491272 p.Asp164Tyr missense_variant 0.2
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 575694 p.Pro116Leu missense_variant 0.4
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 0.8
rpoC 763772 p.Val135Met missense_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765155 p.Thr596Leu missense_variant 0.67
rpoC 766619 p.Gln1084Lys missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776344 p.Gly713Trp missense_variant 0.33
mmpL5 777344 p.Trp379Cys missense_variant 0.33
mmpR5 778277 c.-713C>A upstream_gene_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800799 c.-10G>T upstream_gene_variant 0.22
fbiC 1302975 c.45C>A synonymous_variant 0.29
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
embR 1416201 p.Gly383Trp missense_variant 0.29
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 1.0
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.62
rrs 1472101 n.256G>A non_coding_transcript_exon_variant 0.77
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.77
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.91
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.96
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.86
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.97
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.97
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.98
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.99
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.99
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.99
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.99
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.99
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.99
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.99
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.99
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.98
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.99
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.97
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.97
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.97
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.94
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.95
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.92
rrs 1472262 n.417C>T non_coding_transcript_exon_variant 0.91
rrs 1472269 n.424G>A non_coding_transcript_exon_variant 0.69
rrs 1472271 n.426T>C non_coding_transcript_exon_variant 0.69
rrs 1472277 n.432C>A non_coding_transcript_exon_variant 0.43
rrs 1472378 n.533G>T non_coding_transcript_exon_variant 0.43
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.43
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.43
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.43
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.96
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.97
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.99
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.99
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 1.0
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 1.0
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 1.0
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 1.0
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.99
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.99
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.99
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.99
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.96
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.5
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.91
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.95
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.98
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.98
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.99
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.99
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.98
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.98
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.99
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.98
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.9
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.5
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.4
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.4
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.4
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.33
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.29
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.29
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.38
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.5
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.5
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.45
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.2
rrl 1473552 n.-106G>T upstream_gene_variant 0.3
rrl 1473675 n.18C>A non_coding_transcript_exon_variant 0.2
rrl 1473877 n.220G>T non_coding_transcript_exon_variant 0.5
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 1.0
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.88
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.88
rrl 1474824 n.1167A>C non_coding_transcript_exon_variant 0.88
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.88
rrl 1474830 n.1173A>C non_coding_transcript_exon_variant 0.88
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.88
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 0.89
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.89
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.95
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.95
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.95
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.94
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.94
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.94
rrl 1474903 n.1246T>A non_coding_transcript_exon_variant 0.94
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.94
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 1.0
rrl 1474920 n.1263G>C non_coding_transcript_exon_variant 1.0
rrl 1474928 n.1271C>A non_coding_transcript_exon_variant 1.0
rrl 1475574 n.1917C>A non_coding_transcript_exon_variant 0.43
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.67
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.67
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.73
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.73
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.56
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.5
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.33
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.25
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.93
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.95
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.97
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.97
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.97
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.98
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.98
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.98
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.98
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.98
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.98
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.98
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.98
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.98
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.98
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.98
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.98
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.98
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.99
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.99
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.99
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.99
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 1.0
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 1.0
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 1.0
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 1.0
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.99
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 1.0
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 1.0
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 1.0
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 1.0
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 1.0
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.99
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 1.0
rrl 1476519 n.2862C>G 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 0.99
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.99
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.99
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.99
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.98
rrl 1476595 n.2938C>G non_coding_transcript_exon_variant 0.88
rrl 1476596 n.2939C>T non_coding_transcript_exon_variant 0.85
fabG1 1673504 p.Gly22Val missense_variant 0.33
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
inhA 1674904 p.Ala235Thr missense_variant 1.0
rpsA 1834487 p.Gly316Cys missense_variant 0.29
tlyA 1917771 c.-169G>T upstream_gene_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102997 p.Arg16* stop_gained 0.33
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156301 c.-190G>T upstream_gene_variant 0.4
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2222981 p.Ala62Ser missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518336 c.222A>T synonymous_variant 0.2
kasA 2519048 p.Gly312Ser missense_variant 1.0
eis 2714408 p.Gly309Cys missense_variant 0.5
eis 2714933 p.Ala134Ser missense_variant 0.29
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746859 p.Ala247Asp missense_variant 0.29
pepQ 2859415 p.Gly335Asp missense_variant 0.29
ribD 2987339 c.501C>A synonymous_variant 0.18
ribD 2987488 p.Pro217His missense_variant 0.2
Rv2752c 3065023 p.Pro390Gln missense_variant 0.25
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
Rv3083 3449484 p.Lys327Asn missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474729 c.723G>T synonymous_variant 0.29
fprA 3475269 c.1263C>T synonymous_variant 0.29
whiB7 3568488 c.191delG frameshift_variant 1.0
Rv3236c 3612742 c.375C>A synonymous_variant 0.4
Rv3236c 3612784 p.Leu111Phe missense_variant 0.29
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
rpoA 3878020 p.Pro163Gln missense_variant 0.18
rpoA 3878109 p.Lys133Asn missense_variant 0.25
clpC1 4038843 p.Val621Glu missense_variant 0.4
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040677 p.Arg10Ser missense_variant 0.22
panD 4044470 c.-189C>T upstream_gene_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 4243979 c.747C>T synonymous_variant 0.33
embA 4244042 c.810C>T synonymous_variant 0.33
embA 4244828 c.1596G>T synonymous_variant 0.29
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246941 p.Pro143Gln missense_variant 0.33
embB 4247572 c.1059A>G synonymous_variant 0.2
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247806 c.1293G>T synonymous_variant 0.33
aftB 4269324 c.-488C>T upstream_gene_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
ethA 4326013 c.1461G>T synonymous_variant 0.17
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