Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A4 F13 I0 R1	140	52.5	2164708	98.8%	2138731	146.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947_CJ‑RC	5,684,230:1	+CGGG	100%	intergenic (‑133/+71)	PP_4986 ← / ← PP_4987	hemolysin III family channel protein/putative Chemotaxis protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947_CJ‑RC	5,684,230	1	.	C	100.0%	15.6 / NA	6	intergenic (‑133/+71)	PP_4986/PP_4987	hemolysin III family channel protein/putative Chemotaxis protein
Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (1/5); total (1/5)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
*	NC_002947_CJ‑RC	5,684,230	2	.	G	100.0%	15.6 / NA	6	intergenic (‑133/+71)	PP_4986/PP_4987	hemolysin III family channel protein/putative Chemotaxis protein
Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (1/5); total (1/5)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
*	NC_002947_CJ‑RC	5,684,230	3	.	G	100.0%	15.4 / NA	6	intergenic (‑133/+71)	PP_4986/PP_4987	hemolysin III family channel protein/putative Chemotaxis protein
Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (1/5); total (1/5)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
*	NC_002947_CJ‑RC	5,684,230	4	.	G	100.0%	15.8 / NA	6	intergenic (‑133/+71)	PP_4986/PP_4987	hemolysin III family channel protein/putative Chemotaxis protein
Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (1/5); total (1/5)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CCGTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGC‑‑‑‑GCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGCCTTTCCAATGCGACCAG  >  NC_002947_CJ‑RC/5684087‑5684357

                                                                                                                                                ||||

ccGTAATACATGCAAACACAGACCTCCTGTGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCTAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACcgccg                                                                                                                                   <  4:9581/146‑3 (MQ=255)

 cGTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACcgccggg                                                                                                                                 <  2:270235/147‑5 (MQ=255)

                   aGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTAt                                                                                                               <  7:182629/147‑1 (MQ=37)

                     aCCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATcg                                                                                                             <  1:159846/147‑1 (MQ=37)

                       ctcctGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATcgcg                                                                                                           <  4:259168/147‑1 (MQ=37)

                                                                                                         gAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGCCGGGGCTGCTGCGCCGCCCAATAGCCACCCAAGGCCCCGCCCCCACCAGACCCCCCCGCCCAGCGCCGCCCAACCAAACCCACGGAAGGTTGCAGATCcccggccccc                         >  2:39270/1‑141 (MQ=255)

                                                                                                                             ttGCCACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGCCTTTCCAATGCGAc     <  1:39270/147‑1 (MQ=38)

                                                                                                                                 cACTGCATGAACCGCCGGGGCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGCCTTTCCAATGCGACCAg  <  3:222290/146‑1 (MQ=38)

                                                                                                                                                ||||

CCGTAATACATGCAAACACAGACCTCCTGAGGTGGGCTGGGTTCCTGTTGTGATGCTGATGGCTTCGTTCTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGGCGCGAAGCGGCCCCAGGCTTTCATTGCCACTGCATGAACCGC‑‑‑‑GCTGCTGCGCAGCCCTATCGCGACACAAGGCCGCTCCCACTCCAGACCACCAGGCCCTGCGCCTCACATCCTAACCAAGGTCAGGTTGCAGATCCGCGTCACGCACCAGCCTTTCCAATGCGACCAG  >  NC_002947_CJ‑RC/5684087‑5684357

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A