TB-Profiler result

Run: SRR3105762
Summary

Run ID: SRR3105762

Sample name:

Date: 04-04-2023 05:08:15

Number of reads: 304302

Percentage reads mapped: 7.59

Strain:

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
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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.83 isoniazid
pncA 2288764 p.Thr160Pro missense_variant 0.4 pyrazinamide
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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.29
rpoB 760115 c.309C>T synonymous_variant 0.5
rpoB 761850 p.Pro682Ala missense_variant 0.7
rpoC 762899 c.-471G>C upstream_gene_variant 0.5
rpoB 762911 p.Ile1035Met missense_variant 0.4
rpoC 762917 c.-453C>G upstream_gene_variant 0.6
rpoC 762920 c.-450C>T upstream_gene_variant 0.6
rpoC 762923 c.-447C>G upstream_gene_variant 0.6
rpoC 762929 c.-441G>C upstream_gene_variant 0.78
rpoB 762939 p.Met1045Leu missense_variant 0.7
rpoB 762942 p.Ile1046Val missense_variant 0.64
rpoC 762965 c.-405T>C upstream_gene_variant 0.64
rpoC 762980 c.-390T>C upstream_gene_variant 0.5
rpoC 762989 c.-381G>T upstream_gene_variant 0.33
rpoC 762998 c.-372G>A upstream_gene_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 0.5
rpoC 764263 c.894G>A synonymous_variant 0.67
rpoC 764605 c.1236G>C synonymous_variant 1.0
rpoC 764611 c.1242G>C synonymous_variant 1.0
rpoC 764623 c.1254C>G synonymous_variant 1.0
rpoC 764632 c.1263T>C synonymous_variant 1.0
rpoC 764650 c.1281G>T synonymous_variant 0.95
rpoC 764665 c.1296C>G synonymous_variant 0.96
rpoC 764668 c.1299C>T synonymous_variant 0.96
rpoC 764695 c.1326T>C synonymous_variant 0.95
rpoC 764713 c.1344G>C synonymous_variant 0.92
rpoC 764719 c.1350G>A synonymous_variant 0.9
rpoC 764731 c.1362G>T synonymous_variant 0.8
rpoC 764735 p.Val456Met missense_variant 0.67
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.33
mmpL5 777320 c.1161C>G synonymous_variant 0.6
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407537 c.-197G>T 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 0.25
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.25
rrs 1472108 n.263C>A non_coding_transcript_exon_variant 0.25
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.38
rrs 1472128 n.283G>C non_coding_transcript_exon_variant 0.38
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.38
rrs 1472135 n.290C>T non_coding_transcript_exon_variant 0.3
rrs 1472138 n.293C>T non_coding_transcript_exon_variant 0.27
rrs 1472139 n.294C>T non_coding_transcript_exon_variant 0.27
rrs 1472147 n.302G>A non_coding_transcript_exon_variant 0.3
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.3
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.3
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.67
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.82
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.91
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.93
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.88
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.87
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.86
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.88
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.86
rrs 1472243 n.398G>C non_coding_transcript_exon_variant 0.86
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.86
rrs 1472253 n.408G>C non_coding_transcript_exon_variant 0.86
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.89
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.57
rrs 1472279 n.434T>A non_coding_transcript_exon_variant 0.4
rrs 1472328 n.483G>C non_coding_transcript_exon_variant 0.38
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 0.5
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.57
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.73
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.6
rrs 1472390 n.545T>A non_coding_transcript_exon_variant 0.6
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.6
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.5
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.92
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.9
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.93
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.91
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.91
rrs 1472785 n.940G>T non_coding_transcript_exon_variant 0.91
rrs 1472786 n.941C>G non_coding_transcript_exon_variant 0.91
rrs 1472814 n.969G>A non_coding_transcript_exon_variant 0.77
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.33
rrs 1472956 n.1111T>A non_coding_transcript_exon_variant 0.33
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.22
rrs 1473038 n.1193A>C non_coding_transcript_exon_variant 0.31
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.29
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.18
rrs 1473054 n.1209C>G non_coding_transcript_exon_variant 0.18
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.18
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.22
rrs 1473070 n.1225G>C non_coding_transcript_exon_variant 0.22
rrs 1473071 n.1226C>A non_coding_transcript_exon_variant 0.22
rrs 1473139 n.1294T>C non_coding_transcript_exon_variant 0.6
rrs 1473147 n.1302G>C non_coding_transcript_exon_variant 0.8
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.82
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.94
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 0.94
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.97
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.95
rrs 1473204 n.1359C>T non_coding_transcript_exon_variant 0.93
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.93
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.88
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.38
rrs 1473328 n.1483C>T non_coding_transcript_exon_variant 0.33
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.72
rrl 1475632 n.1975C>T non_coding_transcript_exon_variant 0.22
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.55
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 0.7
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.7
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.78
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.79
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.88
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.88
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.86
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.86
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.87
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.89
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.89
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.89
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.88
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.91
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.92
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.9
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.9
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.91
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.9
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.86
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.86
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.9
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.91
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.93
rrl 1476483 n.2826G>A non_coding_transcript_exon_variant 0.9
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.88
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.88
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.87
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.91
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.91
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.91
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.91
rrl 1476528 n.2871A>T non_coding_transcript_exon_variant 0.91
rrl 1476535 n.2878G>C non_coding_transcript_exon_variant 0.86
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.87
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.88
rrl 1476545 n.2888C>T non_coding_transcript_exon_variant 0.88
rrl 1476565 n.2908G>A non_coding_transcript_exon_variant 0.81
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.75
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.67
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.73
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.62
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
thyX 3067452 p.Lys165Thr missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
ddn 3987259 p.Trp139* stop_gained 0.6
clpC1 4039522 c.1183C>T synonymous_variant 0.33
clpC1 4039528 c.1177C>A synonymous_variant 0.5
clpC1 4039541 c.1164C>G synonymous_variant 0.5
clpC1 4039544 c.1161C>T synonymous_variant 0.67
clpC1 4039559 c.1146C>G synonymous_variant 0.33
clpC1 4039674 p.Pro344Lys missense_variant 0.29
clpC1 4039691 c.1014G>C synonymous_variant 0.55
clpC1 4039748 c.957G>C synonymous_variant 0.43
clpC1 4040032 p.Val225Ile missense_variant 0.5
clpC1 4040033 c.672G>C synonymous_variant 0.5
clpC1 4040036 c.669C>T synonymous_variant 0.5
clpC1 4040045 c.660C>G synonymous_variant 0.5
clpC1 4040054 c.651G>A synonymous_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249757 p.Thr1082Ala missense_variant 0.67
ubiA 4269307 p.Phe176Ser missense_variant 0.8
ethA 4326197 p.Val426Gly missense_variant 0.8
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.6