TB-Profiler result

Run: ERR6052085
Summary

Run ID: ERR6052085

Sample name:

Date: 02-04-2023 01:41:14

Number of reads: 1069986

Percentage reads mapped: 24.92

Strain: lineage2.2.2

Drug-resistance: Pre-XDR-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
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.87 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.86 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289202 p.Cys14Arg missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326333 p.Ala381Pro missense_variant 0.97 ethionamide
gid 4407967 p.Leu79Ser missense_variant 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 6554 p.Pro439Ser missense_variant 0.12
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 1.0
rpoB 761877 p.Glu691Lys missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763486 c.117T>C synonymous_variant 0.15
rpoC 763501 p.Asp44Glu missense_variant 0.18
rpoC 763504 c.135C>G synonymous_variant 0.19
rpoC 763507 c.138G>C synonymous_variant 0.19
rpoC 763525 c.156C>T synonymous_variant 0.16
rpoC 763528 c.159G>C synonymous_variant 0.16
rpoC 763534 c.165T>C synonymous_variant 0.16
rpoC 763535 p.Arg56Lys missense_variant 0.14
rpoC 763540 c.171C>T synonymous_variant 0.15
rpoC 763550 p.Tyr61His missense_variant 0.17
rpoC 763570 c.201G>C synonymous_variant 0.14
rpoC 763573 c.204G>C synonymous_variant 0.15
rpoC 763597 p.Glu76Asp missense_variant 0.12
rpoC 763609 c.240C>T synonymous_variant 0.15
rpoC 763612 c.243G>A synonymous_variant 0.15
rpoC 763615 c.246G>C synonymous_variant 0.16
rpoC 763621 c.252C>T synonymous_variant 0.17
rpoC 763627 c.258G>A synonymous_variant 0.16
rpoC 763633 c.264T>C synonymous_variant 0.16
rpoC 763636 c.267T>C synonymous_variant 0.16
rpoC 763642 c.273G>C synonymous_variant 0.17
rpoC 763648 c.279C>A synonymous_variant 0.14
rpoC 763666 c.297G>T synonymous_variant 0.14
rpoC 763669 c.300C>T synonymous_variant 0.14
rpoC 763673 p.Thr102Ser missense_variant 0.14
rpoC 763678 c.309C>T synonymous_variant 0.14
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 767191 c.3822C>G synonymous_variant 0.12
rpoC 767197 c.3828G>A synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472089 n.244C>T non_coding_transcript_exon_variant 0.15
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.29
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.18
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.48
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.48
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.48
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.55
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.56
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.59
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.64
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.65
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.76
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.67
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.67
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.67
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.65
rrs 1472222 n.377G>A non_coding_transcript_exon_variant 0.61
rrs 1472229 n.384C>T non_coding_transcript_exon_variant 0.57
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.58
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.59
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.58
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.38
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.35
rrs 1472256 n.411T>G non_coding_transcript_exon_variant 0.35
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.35
rrs 1472271 n.426T>C non_coding_transcript_exon_variant 0.15
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.17
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.16
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.23
rrs 1472518 n.673G>C non_coding_transcript_exon_variant 0.21
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.36
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.37
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.37
rrs 1472544 n.699C>G non_coding_transcript_exon_variant 0.38
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.38
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.67
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.7
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.7
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.7
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.7
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.72
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.67
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.12
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.15
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.64
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.64
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.64
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.62
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.62
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.59
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.62
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.62
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.6
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.56
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.53
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.12
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.17
rrs 1473020 n.1175T>C non_coding_transcript_exon_variant 0.23
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.36
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.68
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.69
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.69
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.68
rrs 1473070 n.1225G>A non_coding_transcript_exon_variant 0.7
rrs 1473089 n.1244A>C non_coding_transcript_exon_variant 0.72
rrs 1473094 n.1249T>C non_coding_transcript_exon_variant 0.71
rrs 1473099 n.1254T>A non_coding_transcript_exon_variant 0.72
rrs 1473109 n.1264T>C non_coding_transcript_exon_variant 0.68
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.66
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.66
rrs 1473115 n.1270G>C non_coding_transcript_exon_variant 0.69
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.74
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.74
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.74
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.74
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.77
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.77
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.77
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.78
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.77
rrs 1473179 n.1334C>T non_coding_transcript_exon_variant 0.78
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.78
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.79
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.46
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.12
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.44
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.44
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.48
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.59
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.63
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.66
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.73
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.75
rrl 1474830 n.1173A>C non_coding_transcript_exon_variant 0.73
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.74
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.76
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.75
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.76
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.66
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.58
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.55
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.47
rrl 1474920 n.1263G>A non_coding_transcript_exon_variant 0.41
rrl 1474927 n.1271delC non_coding_transcript_exon_variant 0.29
rrl 1474931 n.1274G>A non_coding_transcript_exon_variant 0.29
rrl 1474938 n.1281G>A non_coding_transcript_exon_variant 0.17
rrl 1475672 n.2015C>G non_coding_transcript_exon_variant 0.21
rrl 1475673 n.2016T>C non_coding_transcript_exon_variant 0.23
rrl 1475687 n.2030C>T non_coding_transcript_exon_variant 0.37
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.43
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.42
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.41
rrl 1475707 n.2050T>A non_coding_transcript_exon_variant 0.39
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.36
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.23
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.33
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.33
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.32
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.33
rrl 1475843 n.2186G>A non_coding_transcript_exon_variant 0.3
rrl 1475849 n.2192G>A non_coding_transcript_exon_variant 0.31
rrl 1475853 n.2196C>T non_coding_transcript_exon_variant 0.32
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.32
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.11
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.14
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.43
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.61
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.57
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.59
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.6
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.58
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.58
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.6
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.57
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.57
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.58
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.59
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.77
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.79
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.81
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.82
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.85
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.85
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.86
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.91
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.92
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.91
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.85
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.83
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.69
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.35
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.32
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.67
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.65
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.65
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.66
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.63
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.62
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.61
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.6
rrl 1476624 n.2967T>A non_coding_transcript_exon_variant 0.61
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.63
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.6
rrl 1476637 n.2980C>G non_coding_transcript_exon_variant 0.56
rrl 1476657 n.3000G>C non_coding_transcript_exon_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2221939 p.Arg409Gln missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519332 c.1218C>A synonymous_variant 0.18
thyA 3073806 c.666C>G synonymous_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.3
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269089 p.Ala249Thr missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0