Run ID: SRR1172713
Sample name:
Date: 03-04-2023 03:08:46
Number of reads: 3278624
Percentage reads mapped: 46.19
Strain: lineage4.4
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.4 | Euro-American | S;T | None | 0.98 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288781 | p.Arg154Met | missense_variant | 0.2 | pyrazinamide |
embB | 4248002 | p.Gln497Lys | missense_variant | 1.0 | ethambutol |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6417 | p.Thr393Asn | missense_variant | 0.14 |
gyrA | 7347 | p.Glu16Gln | missense_variant | 0.12 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8306 | c.1005C>A | synonymous_variant | 0.2 |
gyrA | 8323 | p.Phe341Cys | missense_variant | 0.18 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
gyrA | 9394 | p.Ser698Trp | missense_variant | 0.29 |
fgd1 | 491701 | p.His307Asn | missense_variant | 0.2 |
mshA | 576343 | c.996C>A | synonymous_variant | 0.15 |
rpoB | 760179 | p.Ala125Thr | missense_variant | 0.4 |
rpoB | 760280 | c.474C>A | synonymous_variant | 0.18 |
rpoC | 763421 | p.Glu18* | stop_gained | 0.17 |
rpoC | 764441 | p.Ile358Val | missense_variant | 0.95 |
rpoC | 764611 | c.1242G>C | synonymous_variant | 0.12 |
rpoC | 764632 | c.1263T>C | synonymous_variant | 0.23 |
rpoC | 764656 | c.1287C>G | synonymous_variant | 0.11 |
rpoC | 764745 | p.Arg459Leu | missense_variant | 0.18 |
rpoC | 764840 | p.Ile491Val | missense_variant | 1.0 |
rpoC | 765857 | p.Glu830* | stop_gained | 0.5 |
rpoC | 767236 | p.Glu1289Asp | missense_variant | 0.17 |
rpoC | 767248 | p.Tyr1293* | stop_gained | 0.29 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 0.96 |
mmpL5 | 776554 | p.Gln643Lys | missense_variant | 0.29 |
mmpL5 | 776717 | p.Glu588Asp | missense_variant | 0.29 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rpsL | 781407 | c.-153C>G | upstream_gene_variant | 0.2 |
rpsL | 781627 | p.Ala23Asp | missense_variant | 0.18 |
fbiC | 1303024 | p.Arg32Trp | missense_variant | 0.33 |
fbiC | 1303276 | p.Ala116Thr | missense_variant | 0.2 |
fbiC | 1304711 | p.Ala594Asp | missense_variant | 0.18 |
fbiC | 1304715 | c.1785G>T | synonymous_variant | 0.18 |
fbiC | 1304737 | p.Gly603Cys | missense_variant | 0.17 |
fbiC | 1305058 | p.Tyr710Asn | missense_variant | 0.18 |
embR | 1417422 | c.-75C>A | upstream_gene_variant | 0.2 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.56 |
rrs | 1472214 | n.369C>G | non_coding_transcript_exon_variant | 0.67 |
rrs | 1472235 | n.390G>C | non_coding_transcript_exon_variant | 0.5 |
rrs | 1472240 | n.395G>C | non_coding_transcript_exon_variant | 0.5 |
rrs | 1472242 | n.397C>T | non_coding_transcript_exon_variant | 0.5 |
rrs | 1472251 | n.406G>A | non_coding_transcript_exon_variant | 0.29 |
rrs | 1472253 | n.408G>T | non_coding_transcript_exon_variant | 0.25 |
rrs | 1472259 | n.414C>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472264 | n.419T>C | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472266 | n.421C>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472340 | n.495C>T | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472599 | n.754G>A | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.67 |
rrs | 1472734 | n.889C>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472741 | n.896G>A | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.19 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.47 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.58 |
rrs | 1472803 | n.958T>C | non_coding_transcript_exon_variant | 0.5 |
rrs | 1472812 | n.967A>C | non_coding_transcript_exon_variant | 0.5 |
rrs | 1473192 | n.1347A>G | non_coding_transcript_exon_variant | 0.32 |
rrs | 1473205 | n.1360T>C | non_coding_transcript_exon_variant | 0.4 |
rrl | 1474032 | n.375T>C | non_coding_transcript_exon_variant | 0.4 |
rrl | 1474498 | n.841G>T | non_coding_transcript_exon_variant | 0.25 |
rrl | 1474570 | n.913G>T | non_coding_transcript_exon_variant | 0.67 |
rrl | 1474801 | n.1145delT | non_coding_transcript_exon_variant | 0.29 |
rrl | 1474825 | n.1168G>A | non_coding_transcript_exon_variant | 0.33 |
rrl | 1474828 | n.1171G>C | non_coding_transcript_exon_variant | 0.4 |
rrl | 1474832 | n.1176delG | non_coding_transcript_exon_variant | 0.5 |
rrl | 1474864 | n.1207C>T | non_coding_transcript_exon_variant | 0.5 |
rrl | 1474869 | n.1212G>T | non_coding_transcript_exon_variant | 0.5 |
rrl | 1475149 | n.1492G>T | non_coding_transcript_exon_variant | 0.33 |
rrl | 1475791 | n.2134A>G | non_coding_transcript_exon_variant | 0.5 |
rrl | 1475803 | n.2146T>C | non_coding_transcript_exon_variant | 0.6 |
rrl | 1475804 | n.2147G>C | non_coding_transcript_exon_variant | 0.6 |
rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.67 |
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.67 |
rrl | 1475874 | n.2217C>T | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476007 | n.2350T>A | non_coding_transcript_exon_variant | 0.67 |
rrl | 1476336 | n.2679C>G | non_coding_transcript_exon_variant | 0.88 |
rrl | 1476356 | n.2699C>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476357 | n.2700T>A | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 1.0 |
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.92 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.92 |
rrl | 1476384 | n.2727G>C | non_coding_transcript_exon_variant | 0.85 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.85 |
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.85 |
rrl | 1476428 | n.2771C>A | non_coding_transcript_exon_variant | 0.67 |
rrl | 1476443 | n.2786G>C | non_coding_transcript_exon_variant | 0.75 |
rrl | 1476455 | n.2798C>G | non_coding_transcript_exon_variant | 0.56 |
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.55 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.55 |
rrl | 1476470 | n.2813C>T | non_coding_transcript_exon_variant | 0.55 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.5 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.33 |
fabG1 | 1673229 | c.-211C>A | upstream_gene_variant | 0.15 |
inhA | 1674237 | c.36T>G | synonymous_variant | 0.22 |
rpsA | 1834705 | c.1164C>G | synonymous_variant | 0.13 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
ndh | 2102086 | c.957G>T | synonymous_variant | 0.15 |
ndh | 2102936 | p.Ala36Asp | missense_variant | 0.18 |
katG | 2154443 | p.Lys557Glu | missense_variant | 0.12 |
PPE35 | 2168191 | p.Gly808Cys | missense_variant | 0.18 |
PPE35 | 2168270 | c.2343G>C | synonymous_variant | 0.12 |
PPE35 | 2168691 | p.Leu641Arg | missense_variant | 1.0 |
Rv1979c | 2222692 | c.472delG | frameshift_variant | 0.11 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2288754 | p.Val163Ala | missense_variant | 0.29 |
pncA | 2289118 | p.His42Asn | missense_variant | 0.25 |
pncA | 2289626 | c.-385G>A | upstream_gene_variant | 0.17 |
ahpC | 2726204 | c.12A>C | synonymous_variant | 0.18 |
ahpC | 2726363 | p.Phe57Leu | missense_variant | 0.2 |
folC | 2746949 | p.Ala217Glu | missense_variant | 0.23 |
pepQ | 2859967 | p.Asp151Gly | missense_variant | 1.0 |
pepQ | 2860015 | p.Lys135Thr | missense_variant | 0.12 |
ribD | 2986771 | c.-68C>A | upstream_gene_variant | 0.29 |
ribD | 2987598 | p.Arg254Ser | missense_variant | 0.33 |
Rv2752c | 3065715 | c.477T>C | synonymous_variant | 1.0 |
Rv2752c | 3066203 | c.-12G>T | upstream_gene_variant | 0.17 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3086901 | p.Arg28Ser | missense_variant | 0.33 |
ald | 3086916 | p.Val33Met | missense_variant | 0.2 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
whiB7 | 3568635 | p.Leu15Phe | missense_variant | 0.25 |
whiB7 | 3568685 | c.-6C>T | upstream_gene_variant | 0.22 |
fbiB | 3640758 | c.-777G>T | upstream_gene_variant | 0.22 |
alr | 3840637 | p.Pro262Thr | missense_variant | 0.22 |
ddn | 3986935 | p.Arg31His | missense_variant | 0.22 |
clpC1 | 4039900 | p.Leu269Ile | missense_variant | 0.29 |
clpC1 | 4039931 | c.774T>A | synonymous_variant | 0.2 |
clpC1 | 4040678 | c.27C>A | synonymous_variant | 0.22 |
panD | 4044237 | c.45G>T | synonymous_variant | 0.29 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4245088 | p.Ser619* | stop_gained | 0.22 |
embA | 4245765 | p.Glu845* | stop_gained | 0.23 |
embA | 4246367 | p.Tyr1045* | stop_gained | 0.17 |
embB | 4247947 | c.1434G>A | synonymous_variant | 1.0 |
embB | 4248035 | p.Val508Ile | missense_variant | 0.29 |
embB | 4248131 | p.Arg540Ser | missense_variant | 0.15 |
aftB | 4268523 | p.Leu105Trp | missense_variant | 0.13 |
aftB | 4268928 | c.-92C>T | upstream_gene_variant | 1.0 |
ubiA | 4268948 | p.Gly296Trp | missense_variant | 0.17 |
ubiA | 4269124 | p.Ala237Val | missense_variant | 1.0 |
aftB | 4269375 | c.-539G>A | upstream_gene_variant | 1.0 |
ubiA | 4269662 | p.Ala58Ser | missense_variant | 0.17 |
ubiA | 4269862 | c.-29G>A | upstream_gene_variant | 0.22 |
ubiA | 4269892 | c.-59G>T | upstream_gene_variant | 0.15 |
ubiA | 4269934 | c.-101C>A | upstream_gene_variant | 0.25 |
ubiA | 4269946 | c.-113G>T | upstream_gene_variant | 0.5 |
ethA | 4326181 | p.Phe431Leu | missense_variant | 0.22 |
ethA | 4326205 | c.1269C>A | synonymous_variant | 0.15 |
ethA | 4326719 | p.Ala252Phe | missense_variant | 1.0 |
ethA | 4327547 | c.-74C>A | upstream_gene_variant | 0.15 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |