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
A1 F1 I1 R1	66	46.7	5280542	98.1%	5180211	47.6

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_017635	3,114,884	Δ1 bp	pseudogene (125/2509 nt)	vgrG →	type VI secretion system tip protein VgrG

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_017635	3,114,883	0	C	.	100.0%	35.6 / NA	25	pseudogene (124/2509 nt)	vgrG	type VI secretion system tip protein VgrG
Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (7/18); total (7/18)

AAGGCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATTCCAGTTTACCAGTACCGATAAAGCCATCACGCCGGAGTTGGTGC  >  NC_017635/3114842‑3114926

aaGGCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTa                                      <  1:291104/48‑1 (MQ=11)

aaGGCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTa                                      <  1:794245/48‑1 (MQ=11)

 aGGCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTAc                                     <  2:459767/48‑1 (MQ=11)

  ggCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTAcc                                    <  2:892787/48‑1 (MQ=11)

  ggCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTAcc                                    <  1:2336808/48‑1 (MQ=11)

  ggCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTAcc                                    <  2:2085111/48‑1 (MQ=11)

  ggCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTAcc                                    <  2:1543485/48‑1 (MQ=11)

  ggCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTAc                                     >  2:733513/1‑47 (MQ=11)

  ggCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTAc                                     >  2:1751613/1‑47 (MQ=11)

   gCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTACCa                                   <  1:2347453/48‑1 (MQ=11)

   gCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTACCa                                   <  2:2292513/48‑1 (MQ=11)

   gCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTACCa                                   <  2:1800308/48‑1 (MQ=11)

   gCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTACCa                                   <  2:1497390/48‑1 (MQ=11)

         aacaacTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTACCAGTACCg                             <  2:665286/48‑1 (MQ=11)

               tGAGTACCCCGTTCCGCTACGACATT‑CAGTTTACCAGTACCGATAAAg                       >  1:853669/1‑48 (MQ=11)

                 aGTACCCCGTTCCGCTACGACATT‑CAGTTTACCAGTACCGATAAAGc                      >  1:1511483/1‑47 (MQ=11)

                     ccccGTTCCGCTACGACATT‑CAGTTTACCAGTACCGATAAAGCCATc                  <  2:1356671/47‑1 (MQ=11)

                     ccccGTTCCGCTACGACATT‑CAGTTTACCAGTACCGATAAAGCCATc                  <  1:1994777/47‑1 (MQ=11)

                     ccccGTTCCGCTACGACATT‑CAGTTTACCAGTACCGATAAAGCCATc                  <  1:1130299/47‑1 (MQ=11)

                           tCCGCTACGACATT‑CAGTTTACCAGTACCGATAAAGCCATCACGCCg            >  1:734133/1‑47 (MQ=11)

                               cTACGACATT‑CAGTTTACCAGTACCGATAAAGCCATCACGCCGGAGtt       >  1:2224167/1‑48 (MQ=11)

                                  cGACATT‑CAGTTTACCAGTACCGATAAAGCCATCACGCCGGAGTTg      <  2:1765853/46‑1 (MQ=11)

                                  cGACATT‑CAGTTTACCAGTACCGATAAAGCCATCACGCCGGAGTTg      <  1:2550254/46‑1 (MQ=11)

                                   gACATT‑CAGTTTACCAGTACCGATAAAGCCATCACGCCGGAGTTGGTg   >  2:1301188/1‑48 (MQ=11)

                                    aCATT‑CAGTTTACCAGTACCGATAAAGCCATCACGCCGGAGTTGGTGc  <  1:1700587/48‑1 (MQ=1)

AAGGCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATTCCAGTTTACCAGTACCGATAAAGCCATCACGCCGGAGTTGGTGC  >  NC_017635/3114842‑3114926

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

N/A