TB-Profiler result

Run: SRR1062867
Summary

Run ID: SRR1062867

Sample name:

Date: 02-04-2023 18:37:35

Number of reads: 145988

Percentage reads mapped: 1.89

Strain: lineage4.9;lineage2.2.1

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 0.98
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.1
lineage4.9 Euro-American (H37Rv-like) T1 None 0.92
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
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
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
rpoB 762879 p.Met1025Leu missense_variant 0.75
rpoC 762887 c.-483G>C upstream_gene_variant 0.27
rpoB 762894 p.Leu1030Phe missense_variant 0.67
rpoC 762899 c.-471G>C upstream_gene_variant 0.73
rpoB 762911 p.Ile1035Met missense_variant 0.79
rpoC 762917 c.-453C>G upstream_gene_variant 0.96
rpoC 762920 c.-450C>T upstream_gene_variant 0.92
rpoC 762923 c.-447C>G upstream_gene_variant 0.96
rpoB 762925 p.Thr1040Ile missense_variant 0.17
rpoC 762929 c.-441G>T upstream_gene_variant 0.95
rpoC 762932 c.-438G>C upstream_gene_variant 0.17
rpoB 762939 p.Met1045Leu missense_variant 0.96
rpoB 762942 p.Ile1046Val missense_variant 0.96
rpoC 762947 c.-423C>G upstream_gene_variant 0.79
rpoC 762965 c.-405T>C upstream_gene_variant 0.17
rpoC 762971 c.-399G>C upstream_gene_variant 0.78
rpoC 762980 c.-390T>C upstream_gene_variant 0.19
rpoC 762989 c.-381G>T upstream_gene_variant 0.88
rpoC 762995 c.-375G>T upstream_gene_variant 0.75
rpoC 762998 c.-372G>A upstream_gene_variant 0.67
rpoC 763031 c.-339T>C upstream_gene_variant 0.67
rpoC 764557 p.Asn396Lys missense_variant 0.4
rpoC 764575 c.1206T>G synonymous_variant 0.6
rpoC 764581 c.1212T>C synonymous_variant 0.5
rpoC 764582 p.Leu405Met missense_variant 0.5
rpoC 764605 c.1236G>C synonymous_variant 0.62
rpoC 764611 c.1242G>T synonymous_variant 0.62
rpoC 764623 c.1254C>G synonymous_variant 0.47
rpoC 764632 c.1263T>C synonymous_variant 0.82
rpoC 764635 c.1266C>G synonymous_variant 0.48
rpoC 764641 c.1272C>T synonymous_variant 0.32
rpoC 764650 c.1281G>T synonymous_variant 0.73
rpoC 764663 p.Val432Thr missense_variant 0.26
rpoC 764668 c.1299C>T synonymous_variant 0.26
rpoC 764672 p.Gln435Ala missense_variant 0.81
rpoC 764686 c.1317C>T synonymous_variant 0.73
rpoC 764695 c.1326T>C synonymous_variant 0.89
rpoC 764701 c.1332C>G synonymous_variant 0.22
rpoC 764705 p.Leu446Lys missense_variant 0.24
rpoC 764716 c.1347G>C synonymous_variant 0.83
rpoC 764719 c.1350G>A synonymous_variant 0.56
rpoC 764722 c.1353G>C synonymous_variant 0.62
rpoC 764731 c.1362G>C synonymous_variant 0.5
rpoC 764902 c.1533C>G synonymous_variant 0.75
rpoC 764911 c.1542A>G synonymous_variant 0.75
rpoC 764912 p.Met515Val missense_variant 0.78
rpoC 764918 p.Val517Ile missense_variant 0.78
rpoC 764935 c.1566T>C synonymous_variant 0.78
rpoC 764948 c.1579T>C synonymous_variant 0.86
rpoC 764953 c.1584G>C synonymous_variant 0.86
rpoC 764956 c.1587T>C synonymous_variant 0.86
rpoC 764958 p.Glu530Ala missense_variant 0.86
rpoC 764968 c.1599T>C synonymous_variant 0.86
mmpL5 776061 p.Thr807Ser missense_variant 0.33
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781679 c.120C>G synonymous_variant 0.5
rpsL 781682 c.123T>G synonymous_variant 0.5
fbiC 1304271 c.1341C>T synonymous_variant 0.33
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 0.86
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.97
rrs 1472210 n.365A>T non_coding_transcript_exon_variant 0.84
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.99
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.66
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.66
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.94
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.94
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.94
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.9
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.21
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.72
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.59
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.91
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.65
rrs 1472279 n.434T>A non_coding_transcript_exon_variant 0.42
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 0.5
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.44
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.33
rrs 1472402 n.557G>A non_coding_transcript_exon_variant 0.25
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.25
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.5
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.29
rrs 1472707 n.862A>G non_coding_transcript_exon_variant 0.2
rrs 1472709 n.864T>G non_coding_transcript_exon_variant 0.2
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.2
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.7
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.5
rrs 1472716 n.871C>A non_coding_transcript_exon_variant 0.33
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.73
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.74
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.96
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.2
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.76
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.97
rrs 1472785 n.940G>T non_coding_transcript_exon_variant 0.75
rrs 1472786 n.941C>G non_coding_transcript_exon_variant 0.75
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.41
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.18
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.17
rrs 1472814 n.969G>A non_coding_transcript_exon_variant 0.81
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.25
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.38
rrs 1472826 n.981G>C non_coding_transcript_exon_variant 0.8
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.5
rrs 1472911 n.1066T>C non_coding_transcript_exon_variant 0.3
rrs 1472918 n.1073A>G non_coding_transcript_exon_variant 0.27
rrs 1472951 n.1106T>C non_coding_transcript_exon_variant 0.3
rrs 1472955 n.1110C>A non_coding_transcript_exon_variant 0.38
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.38
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.75
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.75
rrs 1472972 n.1127T>A non_coding_transcript_exon_variant 0.33
rrs 1472973 n.1128A>C non_coding_transcript_exon_variant 0.5
rrs 1472974 n.1130_1133delTGGT non_coding_transcript_exon_variant 0.4
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.67
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.75
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.75
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.83
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.83
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.83
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.83
rrs 1473038 n.1193A>C non_coding_transcript_exon_variant 0.83
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.83
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.8
rrs 1473054 n.1209C>G non_coding_transcript_exon_variant 0.83
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.67
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.4
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 1.0
rrs 1473070 n.1225G>C non_coding_transcript_exon_variant 0.67
rrs 1473071 n.1226C>A non_coding_transcript_exon_variant 0.67
rrs 1473139 n.1294T>C non_coding_transcript_exon_variant 1.0
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.93
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.94
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.91
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.9
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.85
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.85
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.97
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.97
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.97
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.91
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.71
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.75
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.29
rrl 1475787 n.2130C>T non_coding_transcript_exon_variant 0.27
rrl 1475790 n.2133C>A non_coding_transcript_exon_variant 0.18
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 0.5
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 0.73
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.73
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.4
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.6
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.6
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.71
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.92
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.82
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.91
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.9
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.95
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.78
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.93
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.79
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.96
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.84
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.89
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.92
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.94
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.8
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.77
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.76
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.94
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.93
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.76
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.84
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.87
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.85
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.18
rrl 1476483 n.2826G>A non_coding_transcript_exon_variant 0.75
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.23
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.78
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.82
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.5
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.6
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.5
fabG1 1673276 c.-164G>A upstream_gene_variant 0.5
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.8
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747464 c.135G>T synonymous_variant 1.0
thyA 3073953 c.519T>C synonymous_variant 0.75
thyA 3073956 c.516G>C synonymous_variant 0.75
thyA 3073959 c.513T>C synonymous_variant 0.82
thyA 3073962 p.Leu170Ile missense_variant 0.82
thyA 3073977 c.495A>G synonymous_variant 0.82
thyA 3073989 c.483T>C synonymous_variant 0.82
thyA 3073992 c.478_480delAGCinsTCG synonymous_variant 0.82
thyA 3073999 p.Arg158Lys missense_variant 0.9
thyA 3074004 c.468T>C synonymous_variant 0.9
thyA 3074010 c.462C>G synonymous_variant 0.9
thyA 3074031 c.441T>C synonymous_variant 0.8
thyA 3074034 c.438T>C synonymous_variant 0.75
ald 3086788 c.-32T>C upstream_gene_variant 1.0
alr 3841356 p.Ser22Leu missense_variant 1.0
rpoA 3877963 p.Arg182Leu missense_variant 1.0
ddn 3986849 c.6G>A synonymous_variant 0.5
embA 4243460 c.228C>T synonymous_variant 1.0
ubiA 4268929 p.Gly302Val missense_variant 0.5
ethA 4327322 p.Pro51His missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.5
gid 4407927 p.Glu92Asp missense_variant 1.0