TB-Profiler result

Run: SRR1173113
Summary

Run ID: SRR1173113

Sample name:

Date: 03-04-2023 03:16:48

Number of reads: 186960

Percentage reads mapped: 1.77

Strain: lineage4.3.4

Drug-resistance: RR-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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 0.06
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
rpoB 761095 p.Leu430Pro missense_variant 1.0 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.99 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 6123 p.Ala295Asp missense_variant 0.67
gyrB 6521 p.Arg428Trp missense_variant 0.67
gyrA 7198 c.-104C>A upstream_gene_variant 0.25
gyrB 7215 p.Arg659Gln missense_variant 0.5
gyrA 7274 c.-28C>A upstream_gene_variant 1.0
gyrA 7342 p.Arg14Gln missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9113 c.1812C>A synonymous_variant 0.67
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490623 c.-160G>T upstream_gene_variant 0.67
fgd1 491288 p.Gly169Asp missense_variant 1.0
mshA 575543 p.Gly66Ser missense_variant 0.67
mshA 576223 c.876G>T synonymous_variant 0.5
mshA 576244 c.897C>A synonymous_variant 0.5
rpoB 759837 p.Ala11Thr missense_variant 0.67
rpoB 759868 p.Ser21Tyr missense_variant 0.5
rpoB 760232 p.Lys142Asn missense_variant 0.29
rpoB 760251 p.Gly149Cys missense_variant 0.33
rpoB 760292 c.486C>A synonymous_variant 0.25
rpoB 761458 p.Pro551Gln missense_variant 0.4
rpoB 761655 p.Ala617Ser missense_variant 0.5
rpoC 762812 c.-558C>A upstream_gene_variant 0.67
rpoC 763405 c.36C>T synonymous_variant 0.33
rpoC 765082 c.1713G>T synonymous_variant 0.67
rpoC 765099 p.Pro577Leu missense_variant 0.67
rpoC 765448 p.Gln693His missense_variant 0.5
mmpL5 776148 p.Ile778Thr missense_variant 0.22
mmpL5 776182 p.Asp767Asn missense_variant 0.22
mmpL5 776483 p.Met666Ile missense_variant 0.33
mmpL5 777856 p.Ala209Ser missense_variant 0.4
mmpS5 779534 c.-629C>A upstream_gene_variant 0.5
rplC 801181 p.Gly125Ser missense_variant 1.0
fbiC 1302825 c.-106C>A upstream_gene_variant 0.67
fbiC 1303226 p.Arg99Leu missense_variant 0.5
fbiC 1303720 p.Gly264Cys missense_variant 0.5
fbiC 1304013 c.1083G>A synonymous_variant 0.5
fbiC 1304028 p.Asn366Lys missense_variant 0.33
embR 1417007 p.Arg114Gln missense_variant 0.67
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471873 n.28C>T non_coding_transcript_exon_variant 0.25
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.6
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.82
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.82
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.82
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.82
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 1.0
rrs 1472128 n.283G>A non_coding_transcript_exon_variant 1.0
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 1.0
rrs 1472130 n.285G>A non_coding_transcript_exon_variant 1.0
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 1.0
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 1.0
rrs 1472498 n.653C>A non_coding_transcript_exon_variant 0.75
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.96
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.98
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.98
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.99
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.99
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.99
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.99
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 1.0
rrs 1472571 n.726G>C 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 1472598 n.753A>C non_coding_transcript_exon_variant 1.0
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 1.0
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 1.0
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.99
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.98
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.98
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.98
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.89
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.97
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.97
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.97
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 0.97
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.98
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.96
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 1472781 n.936C>T non_coding_transcript_exon_variant 0.99
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.99
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.99
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.97
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.92
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.92
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.5
rrs 1472951 n.1106T>C non_coding_transcript_exon_variant 0.5
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.5
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.5
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.5
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.5
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.67
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.67
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 1.0
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 1.0
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.95
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.95
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.95
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.96
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.96
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.96
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.96
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.97
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.88
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.88
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.88
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.29
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.29
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.29
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.29
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.29
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 0.29
rrs 1473316 n.1471C>A non_coding_transcript_exon_variant 0.5
rrs 1473318 n.1473G>A non_coding_transcript_exon_variant 0.5
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.5
rrs 1473327 n.1482A>G non_coding_transcript_exon_variant 0.67
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.67
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.88
rrl 1473869 n.212C>A non_coding_transcript_exon_variant 0.33
rrl 1474233 n.576C>A non_coding_transcript_exon_variant 0.4
rrl 1474584 n.927C>T non_coding_transcript_exon_variant 0.4
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 1.0
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 1.0
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 1.0
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 1.0
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 1.0
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 1.0
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.58
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.58
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.7
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.7
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.78
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.78
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 0.88
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.88
rrl 1474848 n.1191G>A non_coding_transcript_exon_variant 0.88
rrl 1474862 n.1205C>T non_coding_transcript_exon_variant 0.82
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.88
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.93
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.88
rrl 1474903 n.1246T>C non_coding_transcript_exon_variant 0.88
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.88
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.88
rrl 1474920 n.1263G>C non_coding_transcript_exon_variant 0.7
rrl 1475359 n.1702G>T non_coding_transcript_exon_variant 0.4
rrl 1475361 n.1704G>T non_coding_transcript_exon_variant 0.4
rrl 1475634 n.1977G>T non_coding_transcript_exon_variant 0.67
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.5
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.91
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.9
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.9
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.9
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.9
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.87
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.82
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.7
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.21
rrl 1475963 n.2306G>A non_coding_transcript_exon_variant 0.17
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.33
rrl 1476117 n.2460G>T non_coding_transcript_exon_variant 0.5
rrl 1476126 n.2469C>T non_coding_transcript_exon_variant 0.33
rrl 1476130 n.2473G>A non_coding_transcript_exon_variant 0.29
rrl 1476135 n.2478T>C non_coding_transcript_exon_variant 0.29
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.29
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.43
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.43
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 1.0
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 1.0
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.91
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.98
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.99
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.98
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.98
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.99
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.99
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.99
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.99
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.99
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.99
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.99
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.98
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.96
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.9
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.73
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.62
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.62
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.67
rrl 1476608 n.2951C>T non_coding_transcript_exon_variant 0.33
fabG1 1673361 c.-79C>A upstream_gene_variant 0.5
fabG1 1673471 p.Pro11His missense_variant 0.29
inhA 1674213 c.12G>A synonymous_variant 0.67
rpsA 1833937 p.Glu132Asp missense_variant 1.0
rpsA 1834943 p.Ala468Pro missense_variant 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918110 p.Asp57Glu missense_variant 0.5
ndh 2101697 p.Ala449Asp missense_variant 1.0
ndh 2102827 c.216C>T synonymous_variant 0.67
katG 2154522 p.Ser530* stop_gained 0.5
PPE35 2167746 p.Thr956Asn missense_variant 0.29
PPE35 2167985 p.Met876Ile missense_variant 1.0
PPE35 2167997 c.2616G>T synonymous_variant 0.67
PPE35 2168408 c.2205C>A synonymous_variant 0.33
PPE35 2168894 c.1719C>A synonymous_variant 0.29
PPE35 2169416 c.1197G>T synonymous_variant 0.67
PPE35 2169445 p.Gly390Cys missense_variant 0.5
PPE35 2169460 p.Gly385Cys missense_variant 0.5
PPE35 2169551 c.1062C>A synonymous_variant 0.29
PPE35 2169604 p.Gly337Cys missense_variant 0.29
PPE35 2170268 c.345C>T synonymous_variant 0.67
PPE35 2170731 c.-119C>A upstream_gene_variant 0.5
Rv1979c 2221734 c.1431G>T synonymous_variant 0.5
Rv1979c 2222638 p.Ala176Glu missense_variant 0.5
Rv1979c 2223059 p.Pro36Thr missense_variant 0.4
Rv1979c 2223099 c.66C>T synonymous_variant 0.25
Rv1979c 2223293 c.-129A>T upstream_gene_variant 1.0
kasA 2518298 p.Gly62Cys missense_variant 1.0
ahpC 2726597 c.405C>A synonymous_variant 0.5
folC 2746216 p.Phe461Leu missense_variant 1.0
folC 2746707 p.Gln298* stop_gained 0.67
folC 2746780 c.819C>T synonymous_variant 0.4
folC 2747658 c.-60C>A upstream_gene_variant 0.5
ribD 2986923 p.Pro29Ser missense_variant 0.29
ribD 2987017 p.Gly60Val missense_variant 0.67
Rv2752c 3065318 p.Ala292Thr missense_variant 0.5
Rv2752c 3065324 p.Ala290Ser missense_variant 0.5
Rv2752c 3065325 c.867C>T synonymous_variant 0.5
Rv2752c 3065631 c.561C>T synonymous_variant 1.0
Rv2752c 3065878 p.Ser105* stop_gained 0.67
thyX 3067773 p.Ala58Asp missense_variant 0.5
thyA 3074124 c.348G>A synonymous_variant 1.0
thyA 3074666 c.-195G>T upstream_gene_variant 0.25
ald 3086667 c.-153C>G upstream_gene_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087144 p.Asp109Tyr missense_variant 1.0
Rv3083 3449044 p.Val181Ile missense_variant 0.67
fprA 3474803 p.Arg266Leu missense_variant 1.0
whiB7 3568670 p.Leu4Met missense_variant 1.0
Rv3236c 3613105 c.12G>T synonymous_variant 0.5
fbiB 3642709 p.Gly392Val missense_variant 0.5
alr 3840719 c.702A>G synonymous_variant 1.0
alr 3841390 p.Pro11Thr missense_variant 0.25
rpoA 3878169 c.339G>T synonymous_variant 0.5
rpoA 3878336 p.Gly58Cys missense_variant 0.5
clpC1 4039221 p.Pro495Leu missense_variant 1.0
clpC1 4039811 c.894C>T synonymous_variant 0.33
clpC1 4040476 p.His77Tyr missense_variant 0.4
embC 4241116 c.1254C>A synonymous_variant 0.33
embC 4241952 p.Arg697Met missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243517 c.285C>T synonymous_variant 1.0
embA 4246306 p.Ser1025* stop_gained 1.0
embB 4247932 c.1419C>T synonymous_variant 1.0
embB 4248239 p.Gly576Cys missense_variant 0.33
aftB 4267122 p.Arg572Leu missense_variant 0.33
aftB 4268112 p.Ala242Val missense_variant 0.67
aftB 4268402 p.Leu145Phe missense_variant 1.0
ubiA 4269722 p.Ala38Thr missense_variant 1.0
ethA 4326069 p.Arg469Trp missense_variant 0.4
ethA 4326759 p.Arg239Trp missense_variant 0.29
ethA 4327257 p.Gln73Lys missense_variant 0.5
ethA 4327502 c.-29C>A upstream_gene_variant 0.5
ethA 4328013 c.-540G>A upstream_gene_variant 0.4
ethA 4328222 c.-749G>T upstream_gene_variant 1.0
whiB6 4338257 p.Ala89Ser missense_variant 1.0
whiB6 4338313 p.Ala70Glu missense_variant 0.5
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407852 c.351G>T synonymous_variant 0.67