TB-Profiler result

Run: SRR6046096
Summary

Run ID: SRR6046096

Sample name:

Date: 04-04-2023 12:11:08

Number of reads: 377351

Percentage reads mapped: 56.23

Strain: lineage4.1.2.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 0.44 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
gyrA 6904 c.-398C>A upstream_gene_variant 0.17
gyrB 6992 p.Arg585Cys missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7702 p.Leu134Pro missense_variant 0.25
gyrA 7772 c.471C>T synonymous_variant 0.2
gyrA 9233 c.1932C>T synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9536 c.2235C>G synonymous_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575241 c.-107C>T upstream_gene_variant 0.29
mshA 575679 p.Asn111Ser missense_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.22
rpoB 759663 c.-144G>A upstream_gene_variant 0.22
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761825 p.Asn673Lys missense_variant 0.22
rpoC 764656 c.1287C>T synonymous_variant 0.18
rpoC 764662 c.1293G>C synonymous_variant 0.18
rpoC 764677 c.1308C>G synonymous_variant 0.15
rpoC 764678 p.Lys437Gln missense_variant 0.15
rpoC 764706 p.Leu446Gln missense_variant 0.23
rpoC 764713 c.1344G>T synonymous_variant 0.15
rpoC 764731 c.1362G>C synonymous_variant 0.2
rpoC 764737 c.1368G>T synonymous_variant 0.2
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766516 c.3147C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777878 c.603C>T synonymous_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781791 p.Ser78Pro missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.6
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.4
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.5
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.4
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.4
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.4
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.5
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.38
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.44
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.33
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.33
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.33
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.38
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.33
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.33
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.36
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.29
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.21
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.21
rrs 1472668 n.825_829delGGGTT non_coding_transcript_exon_variant 0.23
rrs 1472675 n.830_831insAGAC non_coding_transcript_exon_variant 0.21
rrs 1472680 n.835C>T non_coding_transcript_exon_variant 0.21
rrs 1472682 n.837T>C non_coding_transcript_exon_variant 0.21
rrs 1472683 n.838T>G non_coding_transcript_exon_variant 0.21
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.21
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.23
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.23
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.31
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.29
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.33
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.33
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.5
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.29
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.29
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.29
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.29
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.33
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.33
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.33
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.29
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.33
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.25
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.25
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.25
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.25
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.25
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.25
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.25
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.22
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.22
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.22
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.22
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.22
rrl 1473726 n.69C>A non_coding_transcript_exon_variant 0.2
rrl 1474011 n.354G>A non_coding_transcript_exon_variant 1.0
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.29
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.29
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.25
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.29
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 1.0
rrl 1475754 n.2097G>A non_coding_transcript_exon_variant 1.0
rrl 1475756 n.2099T>C non_coding_transcript_exon_variant 1.0
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 1.0
rrl 1475763 n.2107_2108delAA non_coding_transcript_exon_variant 1.0
rrl 1475774 n.2117C>T non_coding_transcript_exon_variant 1.0
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 1.0
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.4
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.4
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.4
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.29
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 0.29
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.29
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.67
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.64
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.67
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.82
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.9
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.82
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.82
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.82
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.8
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.8
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.73
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.73
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.82
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.82
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.83
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.95
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.95
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.93
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.93
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.81
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.84
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.84
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.84
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.14
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.76
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.78
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.78
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.19
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.71
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.55
rrl 1476513 n.2856G>T non_coding_transcript_exon_variant 0.29
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.29
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.29
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.22
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.22
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.22
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.22
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.22
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.22
rrl 1476542 n.2885T>C non_coding_transcript_exon_variant 0.29
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.25
fabG1 1673250 c.-189delT upstream_gene_variant 0.22
inhA 1673787 c.-415G>C upstream_gene_variant 0.17
rpsA 1834579 c.1038C>A synonymous_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101791 p.Thr418Ala missense_variant 1.0
PPE35 2169128 c.1484dupA frameshift_variant 1.0
Rv1979c 2222797 p.Pro123Leu missense_variant 0.13
Rv1979c 2223237 c.-73C>T upstream_gene_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288966 c.276G>A synonymous_variant 0.13
pncA 2289999 c.-758G>C upstream_gene_variant 0.2
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ahpC 2726341 p.Val50Gly missense_variant 0.27
Rv2752c 3066078 c.113delG frameshift_variant 0.11
thyX 3067406 c.540A>G synonymous_variant 0.18
thyA 3074648 c.-177T>G upstream_gene_variant 0.4
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.22
Rv3083 3448817 p.Asn105Thr missense_variant 0.5
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474204 p.Gln66His missense_variant 0.25
Rv3236c 3612331 c.785delT frameshift_variant 0.13
ddn 3986752 c.-92C>T upstream_gene_variant 0.13
clpC1 4038394 p.Arg771Ser missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.92
aftB 4267514 c.1323G>A synonymous_variant 0.17
aftB 4268958 c.-122A>G upstream_gene_variant 0.17
ubiA 4269864 c.-31C>G upstream_gene_variant 0.29
whiB6 4338480 c.42T>G synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0