TB-Profiler result

Run: SRR13837642
Summary

Run ID: SRR13837642

Sample name:

Date: 03-04-2023 09:14:59

Number of reads: 297564

Percentage reads mapped: 97.23

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) T1 None 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
rpoB 761098 p.Ser431Thr missense_variant 0.14 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
gyrB 5540 p.Thr101Ser missense_variant 1.0
mshA 575869 c.522G>A synonymous_variant 0.18
rpoB 760558 c.753delC frameshift_variant 0.94
rpoB 760611 p.Leu269Val missense_variant 1.0
rpoB 760919 c.1113C>G synonymous_variant 0.22
rpoB 760925 c.1119T>C synonymous_variant 0.22
rpoB 760934 c.1128C>T synonymous_variant 0.22
rpoB 760946 c.1140A>G synonymous_variant 0.22
rpoB 760970 c.1164G>C synonymous_variant 0.22
rpoB 760982 c.1176G>C synonymous_variant 0.25
rpoB 760985 c.1179G>C synonymous_variant 0.25
rpoB 760991 c.1185G>C synonymous_variant 0.22
rpoB 761015 c.1209G>C synonymous_variant 0.22
rpoB 761021 c.1215G>C synonymous_variant 0.25
rpoB 761027 c.1221A>G synonymous_variant 0.18
rpoB 761036 c.1230G>C synonymous_variant 0.2
rpoB 761037 c.1231T>C synonymous_variant 0.2
rpoB 761051 c.1245G>T synonymous_variant 0.18
rpoB 761094 c.1288C>T synonymous_variant 0.14
rpoB 761102 c.1296A>G synonymous_variant 0.14
rpoB 761133 c.1327_1329delTTGinsCTC synonymous_variant 0.15
rpoB 761150 c.1344A>C synonymous_variant 0.15
rpoB 761165 c.1359G>C synonymous_variant 0.17
rpoB 762490 p.Val895Gly missense_variant 1.0
rpoC 762929 c.-441G>C upstream_gene_variant 0.17
rpoC 762989 c.-381G>C upstream_gene_variant 0.15
rpoC 763402 c.33C>G synonymous_variant 0.12
rpoC 763411 c.42T>G synonymous_variant 0.12
rpoC 765707 c.2340delA frameshift_variant 1.0
fbiC 1303695 c.765T>C synonymous_variant 0.13
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.15
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.11
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.11
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.24
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.12
rrl 1476025 n.2368G>T non_coding_transcript_exon_variant 0.12
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.12
rrl 1476032 n.2375C>A non_coding_transcript_exon_variant 0.12
rrl 1476033 n.2376T>C non_coding_transcript_exon_variant 0.13
rrl 1476034 n.2377C>A non_coding_transcript_exon_variant 0.13
rrl 1476045 n.2388G>T non_coding_transcript_exon_variant 0.13
rrl 1476047 n.2390G>T non_coding_transcript_exon_variant 0.13
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.14
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.19
rrl 1476089 n.2432T>C non_coding_transcript_exon_variant 0.19
rrl 1476095 n.2438C>G non_coding_transcript_exon_variant 0.15
rpsA 1833724 c.183C>G synonymous_variant 0.22
rpsA 1833727 c.186G>C synonymous_variant 0.22
rpsA 1833742 c.201A>G synonymous_variant 0.29
rpsA 1833745 c.204G>C synonymous_variant 0.29
rpsA 1833787 c.246C>G synonymous_variant 0.2
rpsA 1833790 c.249T>A synonymous_variant 0.2
rpsA 1833799 c.258C>G synonymous_variant 0.22
rpsA 1833811 c.270G>C synonymous_variant 0.25
rpsA 1833847 c.306C>G synonymous_variant 0.2
rpsA 1833856 c.315A>G synonymous_variant 0.2
rpsA 1833862 c.321G>T synonymous_variant 0.2
rpsA 1833874 c.333T>C synonymous_variant 0.2
rpsA 1834606 c.1065C>G synonymous_variant 0.17
rpsA 1834609 c.1068T>C synonymous_variant 0.18
rpsA 1834622 c.1081_1083delTCGinsAGC synonymous_variant 0.18
rpsA 1834633 c.1092A>G synonymous_variant 0.2
rpsA 1834639 c.1098T>C synonymous_variant 0.2
rpsA 1834666 c.1125G>C synonymous_variant 0.18
rpsA 1834669 c.1128G>C synonymous_variant 0.18
rpsA 1834688 c.1147_1149delAGTinsTCC synonymous_variant 0.18
ndh 2101690 p.Glu451Asp missense_variant 1.0
PPE35 2168961 p.Gly551Val missense_variant 1.0
Rv1979c 2222084 p.Leu361Ile missense_variant 1.0
Rv1979c 2222431 p.Met245Arg missense_variant 1.0
folC 2747264 p.Gly112Ala missense_variant 0.15
folC 2747275 c.324T>C synonymous_variant 0.14
folC 2747281 c.318A>G synonymous_variant 0.15
folC 2747289 p.Pro104Ala missense_variant 0.15
folC 2747290 c.309A>C synonymous_variant 0.15
folC 2747293 c.306G>A synonymous_variant 0.15
folC 2747302 c.297A>G synonymous_variant 0.15
folC 2747314 c.285A>C synonymous_variant 0.13
folC 2747317 c.282C>G synonymous_variant 0.13
folC 2747355 p.Val82Ile missense_variant 0.15
folC 2747359 c.240C>G synonymous_variant 0.15
folC 2747362 c.237G>C synonymous_variant 0.18
ald 3087020 c.201C>T synonymous_variant 1.0
alr 3841157 c.264A>G synonymous_variant 1.0
rpoA 3877656 c.852T>C synonymous_variant 0.2
rpoA 3878047 p.Ala154Asp missense_variant 0.88
rpoA 3878118 c.390T>C synonymous_variant 0.2
clpC1 4038740 c.1965G>C synonymous_variant 0.22
clpC1 4038748 p.Arg653Cys missense_variant 0.18
clpC1 4038755 c.1950G>C synonymous_variant 0.18
clpC1 4039517 c.1188C>G synonymous_variant 0.2
clpC1 4039526 c.1179G>C synonymous_variant 0.2
clpC1 4039576 p.Ala377Ser missense_variant 0.22
clpC1 4039577 c.1128T>C synonymous_variant 0.22
clpC1 4039586 c.1119G>C synonymous_variant 0.18
clpC1 4039610 c.1095G>C synonymous_variant 0.15
clpC1 4039616 c.1089G>C synonymous_variant 0.14
clpC1 4039622 c.1083C>G synonymous_variant 0.14
clpC1 4039831 c.874T>C synonymous_variant 0.2
clpC1 4039832 c.873C>G synonymous_variant 0.2
clpC1 4039850 c.855T>C synonymous_variant 0.22
embC 4241951 c.2089A>C synonymous_variant 0.2
embB 4247452 c.939C>T synonymous_variant 1.0
ethR 4326799 c.-750G>A upstream_gene_variant 1.0