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
A0 F0 I1 R1	61	39.0	4165548	97.4%	4057243	49.6

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_017635	3,127,359	C→T	pseudogene (675/1425 nt)	tssA →	type VI secretion system protein TssA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_017635	3,127,359	0	C	T	75.0%	10.4 / 4.3	12	pseudogene (675/1425 nt)	tssA	type VI secretion system protein TssA
Reads supporting (aligned to +/- strand): ref base C (2/1); new base T (6/3); total (8/4)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.11e-01

TGTGGACGGCAAAACCCGGCTGGCCCCGCCGCGCACCGAGTCACGCAACCAGCTTAAGCGGCTGTATGCCCAGCAGAACTGGACGGAACTGCTG  >  NC_017635/3127311‑3127404

tgtgGCCGCAAAATCCGGGCGGGCCCCGCCGCGCACCGAGTCACGCAAcc                                              <  2:292293/50‑1 (MQ=9)

 gtgGACGGAAAACCCCGGCTGGCCCCGCCGCGCACCGAGTCACGCAAcc                                              <  2:1383937/49‑1 (MQ=14)

       ggCAAAACCCGGCTGGTCCCGCCGCGCACCGAGTCACGCAATCAGCtt                                         >  1:1354080/1‑48 (MQ=11)

       ggCAAAACCCGGCTGGCCCCGCCGCGCACCGAGTCACGCAACCAGCtt                                         >  1:1641102/1‑48 (MQ=255)

         cAAACCCCGGCTGGTCCCGCCGCGCACCGAGTCACGCAATCAGCTTAAGc                                     <  2:660221/50‑1 (MQ=11)

               ccGGCTGGTCCCGCCGCGCACCGAGTCACGCAATCAGCTTAAGCGGCTGt                               <  1:1861157/50‑1 (MQ=11)

                 ggCTGGCCCCGCCGCGCACCGAGTCACGCAACCAGCTTAAGCGGCTGTAt                             >  2:1977218/1‑50 (MQ=255)

                   cTGGTCCCGCCGCGCACCGAGTCACGCAATCAGCTTAAGCGGCTGTATGc                           >  1:1446135/1‑50 (MQ=11)

                   cTGGCCCCGCCGCGCACCGAGTCACGCAATCAGCTTAAGCGGCTGTATGc                           <  2:794644/50‑1 (MQ=255)

                     ggCCCCGCCGCGCACCGAGTCACGCAACCAGCTTAAGCGGCTGTATGcgc                         <  2:633960/50‑3 (MQ=17)

                                     gAGTCACGCAATCAGCTTAAGCGGCTGTATGCCCAGCAGAACTGGACgg          >  2:1478887/1‑49 (MQ=255)

                                       gTCACGCAATCAGCTTAAGCGGCTGTATGCCCAGCAGAACTGGACGGAAc       >  2:1563272/1‑50 (MQ=255)

                                       gTCACGCAATCAGCTTAAGCGGCTGTATGCCCAGCAGAACTGGACGGAAc       >  2:569208/1‑50 (MQ=255)

                                             cAATCAGCTTAAGCGGCTGTATGCCCAGCAGAACTGGACGGAActgctg  >  2:1526738/1‑49 (MQ=255)

TGTGGACGGCAAAACCCGGCTGGCCCCGCCGCGCACCGAGTCACGCAACCAGCTTAAGCGGCTGTATGCCCAGCAGAACTGGACGGAACTGCTG  >  NC_017635/3127311‑3127404

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

N/A