Analysis Summary

This report aggregates results from rMAP modules (QC, assembly/annotation, pangenome/phylogeny, AMR/MGE/virulence/BLAST, and phylogeny).

Quality Control

Per-sample QC reports

QC Report 1 — A55737
QC Report 2 — A55743
QC Report 3 — A55743
QC Report 4 — A55759
QC Report 5 — A55759
QC Report 6 — A55769
QC Report 7 — A55769
QC Report 8 — A55771
QC Report 9 — A55771
QC Report 10 — A55784
QC Report 11 — A55724
QC Report 12 — A55784
QC Report 13 — A55786
QC Report 14 — A55786
QC Report 15 — A55792
QC Report 16 — A55792
QC Report 17 — A55793
QC Report 18 — A55793
QC Report 19 — A55794
QC Report 20 — A55794
QC Report 21 — A55798
QC Report 22 — A55724
QC Report 23 — A55798
QC Report 24 — A55807
QC Report 25 — A55807
QC Report 26 — A55837
QC Report 27 — A55837
QC Report 28 — A55841
QC Report 29 — A55841
QC Report 30 — A55842
QC Report 31 — A55842
QC Report 32 — A55846
QC Report 33 — A55726
QC Report 34 — A55846
QC Report 35 — A55849
QC Report 36 — A55849
QC Report 37 — A55852
QC Report 38 — A55852
QC Report 39 — A55853
QC Report 40 — A55853
QC Report 41 — A55857
QC Report 42 — A55857
QC Report 43 — A55859
QC Report 44 — A55726
QC Report 45 — A55859
QC Report 46 — A55860
QC Report 47 — A55860
QC Report 48 — A55878
QC Report 49 — A55878
QC Report 50 — A55893
QC Report 51 — A55893
QC Report 52 — A55894
QC Report 53 — A55894
QC Report 54 — A55899
QC Report 55 — A55728
QC Report 56 — A55899
QC Report 57 — A55911
QC Report 58 — A55911
QC Report 59 — A55939
QC Report 60 — A55939
QC Report 61 — A55940
QC Report 62 — A55940
QC Report 63 — A55941
QC Report 64 — A55941
QC Report 65 — A55948
QC Report 66 — A55728
QC Report 67 — A55948
QC Report 68 — A55961
QC Report 69 — A55961
QC Report 70 — A55966
QC Report 71 — A55966
QC Report 72 — A56425
QC Report 73 — A56425
QC Report 74 — A56428
QC Report 75 — A56428
QC Report 76 — A55733
QC Report 77 — A55733
QC Report 78 — A55737

Read trimming

Sample	Input Pairs	Both Surviving	Forward Only	Reverse Only	Dropped (%)	Survival Rate (%)
A55724	1543178	1434987	26072	69971	0.79%	99.21%
A55726	1761638	1673784	19970	57627	0.58%	99.42%
A55728	1743635	1637189	26535	65388	0.83%	99.17%
A55733	1422378	1338089	25456	47211	0.82%	99.18%
A55737	1504678	1380613	25860	85399	0.85%	99.15%
A55743	1793305	1697902	19612	63101	0.71%	99.29%
A55759	1130845	1048038	16258	57597	0.79%	99.21%
A55769	1640063	1546591	27436	52193	0.84%	99.16%
A55771	1347045	1249636	19928	67128	0.77%	99.23%
A55784	1274895	1196448	17164	51910	0.74%	99.26%
A55786	1310764	1246232	12020	44538	0.61%	99.39%
A55792	1194394	1085258	34908	59056	1.27%	98.73%
A55793	2604427	2435553	38666	108059	0.85%	99.15%
A55794	2010718	1907408	19726	67493	0.80%	99.20%
A55798	1480019	1416069	19354	32259	0.83%	99.17%
A55807	1119221	1044707	14808	51466	0.74%	99.26%
A55837	1347852	1287030	33244	11828	1.17%	98.83%
A55841	2571794	2450444	17911	87044	0.64%	99.36%
A55842	2184508	2080223	57827	18508	1.28%	98.72%
A55846	1649315	1581752	18495	35365	0.83%	99.17%
A55849	1585004	1517263	36724	15295	0.99%	99.01%
A55852	1786169	1713200	33655	21048	1.02%	98.98%
A55853	1758636	1685775	33553	21533	1.01%	98.99%
A55857	1516056	1448773	34097	15271	1.18%	98.82%
A55859	1945878	1862161	39876	22131	1.12%	98.88%
A55860	1319648	1226661	6923	82751	0.25%	99.75%
A55878	1421785	1353700	11044	46190	0.76%	99.24%
A55893	2217309	2109191	58899	18962	1.36%	98.64%
A55894	2207776	2098285	58965	20330	1.37%	98.63%
A55899	1582087	1501787	44500	13633	1.40%	98.60%
A55911	2026138	1930204	48864	21924	1.24%	98.76%
A55939	2852935	2713862	86760	20340	1.12%	98.88%
A55940	2100917	2004046	52792	21620	1.07%	98.93%
A55941	1733593	1663642	33079	21556	0.88%	99.12%
A55948	2531031	2419659	62890	21722	1.06%	98.94%
A55961	1918626	1825401	54874	16856	1.12%	98.88%
A55966	2428596	2323275	60888	20992	0.97%	99.03%
A56425	1928995	1844169	48948	16721	0.99%	99.01%
A56428	1513687	1447575	32107	19611	0.95%	99.05%

Assembly

Assembly statistics

Sample	Contigs	Total Length	Min Length	Max Length	Avg Length	N50
A55724	131	4934440	435	343169	37667	107645
A55726	64	4741700	476	467429	74089	172156
A55728	80	5176036	432	659027	64700	355426
A55733	94	4933443	432	355995	52483	154283
A55737	115	4574595	428	358727	39779	80136
A55743	137	5046946	505	306082	36839	94756
A55759	80	5186075	459	601831	64826	172464
A55769	3585	10507369	427	48513	2931	5031
A55771	98	5129109	470	301441	52338	120453
A55784	221	5288372	440	243882	23929	95807
A55786	140	5448341	440	351404	38917	179681
A55792	1319	9644116	429	279393	7312	19948
A55793	113	4956357	405	344104	43862	125421
A55794	84	5120256	476	579242	60955	222419
A55798	120	4938774	527	344103	41156	122873
A55807	80	5291220	472	511396	66140	157929
A55837	1760	8955070	449	77359	5088	8804
A55841	90	4677283	529	301635	51970	119856
A55842	89	4989752	482	649161	56065	139439
A55846	90	4633485	450	301622	51483	128930
A55849	117	4884098	472	306090	41744	114390
A55852	66	4790868	476	417672	72589	192728
A55853	130	5627843	487	385753	43291	111681
A55857	2515	7209616	447	59213	2867	4392
A55859	88	4923776	469	401328	55952	136681
A55860	78	5133301	469	640762	65812	269898
A55878	68	4798105	476	619725	70560	336578
A55893	63	5017567	480	806915	79644	319229
A55894	1264	9405895	445	101230	7441	14670
A55899	104	4758194	472	390591	45752	119678
A55911	43	4847524	881	632455	112733	323983
A55939	3293	7429299	445	131389	2256	3137
A55940	53	4675030	472	677242	88208	281447
A55941	1451	5956886	443	134402	4105	17724
A55948	96	5290040	446	530201	55105	195574
A55961	57	4700598	451	429015	82467	192261
A55966	55	4756278	439	711491	86478	244615
A56425	66	4866459	460	405417	73734	205821
A56428	54	5004528	451	806978	92676	353496

Annotation

Annotation summary

Sample ID	Gene Count
A55724	4565
A55726	4410
A55728	4806
A55733	4618
A55737	4271
A55743	4738
A55759	4903
A55769	10000
A55771	4729
A55784	5083
A55786	5190
A55792	9212
A55793	4582
A55794	4819
A55798	4563
A55807	4911
A55837	8265
A55841	4406
A55842	4706
A55846	4337
A55849	4537
A55852	4473
A55853	5322
A55857	6868
A55859	4592
A55860	4809
A55878	4460
A55893	4693
A55894	8804
A55899	4492
A55911	4520
A55939	7244
A55940	4333
A55941	5514
A55948	4967
A55961	4366
A55966	4394
A56425	4553
A56428	4694

Pangenome

Pangenome report

Pangenome Analysis Report

Pangenome Analysis

Roary completed successfully. (This page will show Roary results if available.)

Gene Presence/Absence Heatmap

MLST

Combined MLST

Sample ID	Species	ST	gapA	infB	mdh	pgi	phoE	rpoB	tonB
A55724	ecoli	617	10	11	4	8	8	13	73
A55726	ecoli	2852	6	65	5	1	11	13	6
A55728	ecoli	3910	52	403	76	324	35	40	278
A55733	ecoli	10	10	11	4	8	8	8	2
A55737	ecoli	746	10	7	4	8	12	8	2
A55743	ecoli	1284	10	4	4	8	8	13	73
A55759	ecoli	1193	14	14	10	200	17	7	10
A55769	ecoli	-	14	14	4	8,200	11,12,17	-	10
A55771	ecoli	69	21	35	27	6	5	5	4
A55784	ecoli	-	6	4	12	~774	24	18	7
A55786	ecoli	349	34	36	39	87	67	16	4
A55792	ecoli	448	6	6	5	16	11	8	7
A55793	ecoli	617	10	11	4	8	8	13	73
A55794	ecoli	131	53	40	47	13	36	28	29
A55798	ecoli	617	10	11	4	8	8	13	73
A55807	ecoli	38	4	26	2	25	5	5	19
A55837	ecoli	-	8,21	7,35	1,27	6,8	5,8	5	4
A55841	ecoli	540	6	7	57	1	8	8	2
A55842	ecoli	295	6	4	12	1	9	2	7
A55846	ecoli	540	6	7	57	1	8	8	2
A55849	ecoli	617	10	11	4	8	8	13	73
A55852	ecoli	2852	6	65	5	1	11	13	6
A55853	ecoli	38	4	26	2	25	5	5	19
A55857	senterica	-	621	559	495	~765	~690	~281	636
A55859	ecoli	10	10	11	4	8	8	8	2
A55860	ecoli	131	53	40	47	13	36	28	29
A55878	ecoli	2705	10	11	4	10	7	8	2
A55893	ecoli	1193	14	14	10	200	17	7	10
A55894	senterica	-	621	559,603	554	836	617,690	281,648	700
A55899	ecoli	5455	10	27	5	8	12	8	2
A55911	ecoli	636	13	108	10	97	18	68	93
A55939	senterica	-	621	559	552	765?	617	281	636?
A55940	ecoli	3489	136	7	4	8	8	8	2
A55941	ecoli	3580	6	65	344	1	11	13	6
A55948	ecoli	648	92	4	87	96	70	58	2
A55961	ecoli	10	10	11	4	8	8	8	2
A55966	ecoli	3580	6	65	344	1	11	13	6
A56425	ecoli	410	6	4	12	1	20	18	7
A56428	ecoli	1193	14	14	10	200	17	7	10

Variants

Variant summary

Sample	Status	SNPs	Total Variants	Attempts
A55724	Success	19144	19144	1
A55726	Success	36929	36929	1
A55728	Success	87757	87757	1
A55733	Success	7255	7255	1
A55737	Success	19084	19084	1
A55743	Success	21324	21324	1
A55759	Success	63722	63722	1
A55769	Success	7097	7097	1
A55771	Success	60509	60509	1
A55784	Success	37245	37245	1
A55786	Success	61301	61301	1
A55792	Success	36275	36275	1
A55793	Success	19142	19142	1
A55794	Success	67247	67247	1
A55798	Success	19190	19190	1
A55807	Success	62714	62714	1
A55837	Success	13980	13980	1
A55841	Success	24466	24466	1
A55842	Success	36997	36997	1
A55846	Success	24365	24365	1
A55849	Success	19276	19276	1
A55852	Success	37002	37002	1
A55853	Success	60807	60807	1
A55857	Success	5411	5411	1
A55859	Success	7183	7183	1
A55860	Success	67477	67477	1
A55878	Success	24060	24060	1
A55893	Success	64140	64140	1
A55894	Success	9548	9548	1
A55899	Success	14795	14795	1
A55911	Success	66418	66418	1
A55939	Success	5825	5825	1
A55940	Success	20220	20220	1
A55941	Success	10871	10871	1
A55948	Success	63314	63314	1
A55961	Success	6917	6917	1
A55966	Success	37023	37023	1
A56425	Success	34839	34839	1
A56428	Success	63885	63885	1

Antimicrobial Resistance

Per-sample AMR reports

Mobile Genetic Elements

Per-sample MGE reports

Virulence

Per-sample Virulence reports

BLAST

Per-sample BLAST reports

Phylogeny

core_core_genes.png

rMAP Analysis Pipeline