TB-Profiler result

Run: SRR1013531
Summary

Run ID: SRR1013531

Sample name:

Date: 02-04-2023 15:43:27

Number of reads: 118688

Percentage reads mapped: 1.56

Strain: lineage4.9

Drug-resistance: MDR-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 0.97
lineage4.9 Euro-American (H37Rv-like) T1 None 0.92
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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.14 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289220 p.Asp8Asn missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoC 762894 c.-476C>T upstream_gene_variant 0.88
rpoC 762899 c.-471G>C upstream_gene_variant 0.91
rpoB 762911 p.Ile1035Met missense_variant 0.93
rpoC 762917 c.-453C>G upstream_gene_variant 0.93
rpoC 762920 c.-450C>T upstream_gene_variant 0.93
rpoC 762923 c.-447C>G upstream_gene_variant 0.93
rpoC 762929 c.-441G>T upstream_gene_variant 0.93
rpoB 762939 p.Met1045Leu missense_variant 0.93
rpoB 762942 p.Ile1046Val missense_variant 0.93
rpoC 762947 c.-423C>G upstream_gene_variant 0.87
rpoC 762971 c.-399G>C upstream_gene_variant 0.93
rpoC 762989 c.-381G>T upstream_gene_variant 0.71
rpoC 762995 c.-375G>T upstream_gene_variant 0.6
rpoC 762998 c.-372G>A upstream_gene_variant 0.6
rpoC 763031 c.-339T>C upstream_gene_variant 0.67
rpoC 764521 c.1152T>C synonymous_variant 1.0
rpoC 764536 c.1167G>C synonymous_variant 1.0
rpoC 764537 p.Pro390Thr missense_variant 1.0
rpoC 764540 p.Val391Ile missense_variant 1.0
rpoC 764548 c.1179G>T synonymous_variant 1.0
rpoC 764549 p.Pro394Ala missense_variant 1.0
rpoC 764552 p.Gly395Asn missense_variant 1.0
rpoC 764557 p.Asn396Lys missense_variant 1.0
rpoC 764575 c.1206T>G synonymous_variant 1.0
rpoC 764581 c.1212T>C synonymous_variant 1.0
rpoC 764582 p.Leu405Met missense_variant 1.0
rpoC 764605 c.1236G>C synonymous_variant 1.0
rpoC 764611 c.1242G>T synonymous_variant 1.0
rpoC 764623 c.1254C>G synonymous_variant 0.86
rpoC 764632 c.1263T>C synonymous_variant 0.89
rpoC 764635 c.1266C>G synonymous_variant 0.67
rpoC 764647 c.1278C>T synonymous_variant 0.17
rpoC 764650 c.1281G>T synonymous_variant 1.0
rpoC 764658 c.1289_1290insTAC disruptive_inframe_insertion 0.17
rpoC 764665 c.1296C>G synonymous_variant 1.0
rpoC 764671 c.1302G>A synonymous_variant 0.17
rpoC 764672 p.Gln435Thr missense_variant 1.0
rpoC 764686 c.1317C>T synonymous_variant 0.8
rpoC 764695 c.1326T>C synonymous_variant 0.8
rpoC 764716 c.1347G>C synonymous_variant 0.75
rpoC 764719 c.1350G>A synonymous_variant 0.83
rpoC 764722 c.1353G>C synonymous_variant 1.0
rpoC 764731 c.1362G>C synonymous_variant 1.0
rpoC 764902 c.1533C>G synonymous_variant 1.0
rpoC 764911 c.1542A>G synonymous_variant 1.0
rpoC 764912 p.Met515Val missense_variant 1.0
rpoC 764918 p.Val517Ile missense_variant 1.0
rpoC 764935 c.1566T>C synonymous_variant 1.0
rpoC 764948 c.1579T>C synonymous_variant 1.0
rpoC 764953 c.1584G>C synonymous_variant 0.86
rpoC 764956 c.1587T>C synonymous_variant 1.0
rpoC 764958 p.Glu530Ala missense_variant 1.0
rpoC 764968 c.1599T>C synonymous_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.5
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.96
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.87
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.95
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.71
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.71
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.95
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.92
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.93
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.9
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.85
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.76
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.91
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.5
rrs 1472279 n.434T>A non_coding_transcript_exon_variant 0.4
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.5
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.5
rrs 1472571 n.726G>A non_coding_transcript_exon_variant 0.67
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.5
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.8
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 1.0
rrs 1472709 n.864T>G non_coding_transcript_exon_variant 1.0
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 1.0
rrs 1472715 n.870C>G non_coding_transcript_exon_variant 1.0
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 1.0
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.81
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.81
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 1.0
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.19
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.97
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 1.0
rrs 1472785 n.940G>T non_coding_transcript_exon_variant 0.97
rrs 1472786 n.941C>G non_coding_transcript_exon_variant 0.97
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.23
rrs 1472814 n.969G>A non_coding_transcript_exon_variant 0.95
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.5
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.5
rrs 1472972 n.1127T>A non_coding_transcript_exon_variant 0.5
rrs 1472974 n.1130_1133delTGGT non_coding_transcript_exon_variant 0.5
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.5
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.5
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.5
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.6
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.6
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.6
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.6
rrs 1473139 n.1294T>C non_coding_transcript_exon_variant 0.67
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.78
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>A non_coding_transcript_exon_variant 0.93
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.84
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.84
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 1.0
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 1.0
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.91
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.76
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.67
rrl 1473887 n.230T>A non_coding_transcript_exon_variant 0.67
rrl 1473888 n.231T>A non_coding_transcript_exon_variant 0.67
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.67
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.67
rrl 1475787 n.2130C>T non_coding_transcript_exon_variant 0.67
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.8
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.83
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.83
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 1.0
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 1.0
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.75
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.75
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.8
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.97
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.88
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.89
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.87
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.94
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.87
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.98
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.84
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.98
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.9
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.9
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.9
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.98
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.77
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.76
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.67
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.95
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.95
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.64
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.92
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.88
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.74
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.74
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.33
rrl 1476483 n.2826G>A non_coding_transcript_exon_variant 0.62
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 1.0
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
thyA 3073953 c.519T>C synonymous_variant 0.4
thyA 3073956 c.516G>C synonymous_variant 0.4
thyA 3073959 c.513T>C synonymous_variant 0.5
thyA 3073962 p.Leu170Ile missense_variant 0.5
thyA 3073977 c.495A>G synonymous_variant 0.4
thyA 3073989 c.483T>C synonymous_variant 0.33
thyA 3073992 c.478_480delAGCinsTCG synonymous_variant 0.33
thyA 3073999 p.Arg158Lys missense_variant 0.33
thyA 3074004 c.468T>C synonymous_variant 0.33
thyA 3074010 c.462C>G synonymous_variant 0.33
ald 3086739 c.-81G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala 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