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
A5 F28 I2 R2	154	32.4	3140800	76.4%	2399571	54.5

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	2,099,971	G→A	D156D (GAC→GAT)	cld ←	regulator of length of O‑antigen component of lipopolysaccharide chains

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,099,971	0	G	A	77.8%	46.6 / 10.9	27	D156D (GAC→GAT)	cld	regulator of length of O‑antigen component of lipopolysaccharide chains
Reads supporting (aligned to +/- strand): ref base G (4/2); new base A (0/21); total (4/23)
Fisher's exact test for biased strand distribution p-value = 8.55e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.27e-01

CCAGAGCAATGTTGTCTTTGAGATCCTTTTCTAGCTCTTGATTCACTTTATCGTCAACTTGCTGAATGTATTGGGCCAACTTCATTTGTGCGCCCTCTGCAGTTTGC  >  W3110S.gb/2099919‑2100025

ccAGAGCAATGTTGTCTTTGAGATCCTTTTCTAGCTCTTGATTCACTTTATCGTCAACTTGc                                               <  1:814421/62‑1 (MQ=255)

   gaacAATGTTGTCCTTGAGATCCTTTTCTAGCTCTTGATTCACTTTATCATCAACTTGCTGa                                            <  1:2624962/59‑1 (MQ=255)

   gaacAATGTTGTCCTTGAGATCCTTTTCTAGCTCTTGATTCACTTTATCATCAACTTGCTGa                                            <  1:936538/59‑1 (MQ=255)

   gaacAATGTTGTCCTTGAGATCCTTTTCTAGCTCTTGATTCACTTTATCATCAACTTGCTGa                                            <  1:896754/59‑1 (MQ=255)

   gaacAATGTTGTCCTTGAGATCCTTTTCTAGCTCTTGATTCACTTTATCATCAACTTGCTGa                                            <  1:651088/59‑1 (MQ=255)

   gaacAATGTTGTCCTTGAGATCCTTTTCTAGCTCTTGATTCACTTTATCATCAACTTGCTGa                                            <  1:3035644/59‑1 (MQ=255)

   gaacAATGTTGTCCTTGAGATCCTTTTCTAGCTCTTGATTCACTTTATCATCAACTTGCTGa                                            <  1:2997723/59‑1 (MQ=255)

   gaacAATGTTGTCCTTGAGATCCTTTTCTAGCTCTTGATTCACTTTATCATCAACTTGCTGa                                            <  1:2821482/59‑1 (MQ=255)

   gaacAATGTTGTCCTTGAGATCCTTTTCTAGCTCTTGATTCACTTTATCATCAACTTGCTGa                                            <  1:2799323/59‑1 (MQ=255)

   gaacAATGTTGTCCTTGAGATCCTTTTCTAGCTCTTGATTCACTTTATCATCAACTTGCTGa                                            <  1:2702709/59‑1 (MQ=255)

   gaacAATGTTGTCCTTGAGATCCTTTTCTAGCTCTTGATTCACTTTATCATCAACTTGCTGa                                            <  1:1060394/59‑1 (MQ=255)

   gaacAATGTTGTCCTTGAGATCCTTTTCTAGCTCTTGATTCACTTTATCATCAACTTGCTGa                                            <  1:2360208/59‑1 (MQ=255)

   gaacAATGTTGTCCTTGAGATCCTTTTCTAGCTCTTGATTCACTTTATCATCAACTTGCTGa                                            <  1:2309646/59‑1 (MQ=255)

   gaacAATGTTGTCCTTGAGATCCTTTTCTAGCTCTTGATTCACTTTATCATCAACTTGCTGa                                            <  1:2257330/59‑1 (MQ=255)

   gaacAATGTTGTCCTTGAGATCCTTTTCTAGCTCTTGATTCACTTTATCATCAACTTGCTGa                                            <  1:2154954/59‑1 (MQ=255)

   gaacAATGTTGTCCTTGAGATCCTTTTCTAGCTCTTGATTCACTTTATCATCAACTTGCTGa                                            <  1:2102557/59‑1 (MQ=255)

   gaacAATGTTGTCCTTGAGATCCTTTTCTAGCTCTTGATTCACTTTATCATCAACTTGCTGa                                            <  1:1901952/59‑1 (MQ=255)

   gaacAATGTTGTCCTTGAGATCCTTTTCTAGCTCTTGATTCACTTTATCATCAACTTGCTGa                                            <  1:1879787/59‑1 (MQ=255)

   gaacAATGTTGTCCTTGAGATCCTTTTCTAGCTCTTGATTCACTTTATCATCAACTTGCTGa                                            <  1:1877165/59‑1 (MQ=255)

   gaacAATGTTGTCCTTGAGATCCTTTTCTAGCTCTTGATTCACTTTATCATCAACTTGCTGa                                            <  1:1722531/59‑1 (MQ=255)

   gaacAATGTTGTCCTTGAGATCCTTTTCTAGCTCTTGATTCACTTTATCATCAACTTGCTGa                                            <  1:16186/59‑1 (MQ=255)

   gaacAATGTTGTCCTTGAGATACTTTTCTAGCTCTTGATTCACTTTATCATCAACTTGCTGa                                            <  1:2961433/59‑1 (MQ=255)

        aTGTTGTCTTTGAGATCCTTTTCTAGCTCTTGATTCACTTTATCGTCAACTTGCTGAATGTa                                       <  1:2861014/62‑1 (MQ=255)

                                           cACTTTATCGTCAACTTGCTGAATGTATTGGGCCAACTTCAtt                       >  1:2163205/1‑43 (MQ=255)

                                           cACTTTATCGTCAACTTGCTGAATGTATTGGGCCAACTTCAtt                       >  1:2800814/1‑43 (MQ=255)

                                           cACTTTATCGTCAACTTGCTGAATGTATTGGGCCAACTTCAtt                       >  1:2852906/1‑43 (MQ=255)

                                              tttATCGTCAACTTGCTGAATGTATTGGGCCAACTTCATTTGTGCGCCCTCTGCAGTTTGc  >  1:2572205/1‑61 (MQ=255)

CCAGAGCAATGTTGTCTTTGAGATCCTTTTCTAGCTCTTGATTCACTTTATCGTCAACTTGCTGAATGTATTGGGCCAACTTCATTTGTGCGCCCTCTGCAGTTTGC  >  W3110S.gb/2099919‑2100025

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

N/A