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%	42.6 / NA	29	pseudogene (124/2509 nt)	vgrG	type VI secretion system tip protein VgrG
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (5/24);  total (5/24)

ACCTTCGAAGGCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATTCCAGTTTACCAGTACCGATAAAGCCATCACGCCGGAGTTGGTGCTG  >  NC_017635/3114835‑3114928                                                 |                                              aCCTTCGAAGGCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATTca                                              <  1:1139375/50‑2 (MQ=255) aCCTTCGAAGGCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATTc                                               <  1:389045/49‑1 (MQ=255)      cGAAGGCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATT‑CAGttt                                         <  1:1173223/49‑1 (MQ=11)       gAAGGCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTAc                                       <  1:290379/50‑1 (MQ=11)        aaGGCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTAcc                                      <  2:163545/50‑1 (MQ=11)         aGGCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTAc                                       >  1:563102/1‑48 (MQ=11)         aGGCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTACCa                                     <  1:2059818/50‑1 (MQ=11)          ggCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTACCAg                                    <  1:1250094/50‑1 (MQ=11)           gCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTACCAGt                                   <  2:945812/50‑1 (MQ=11)           gCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTACCAGt                                   <  2:156878/50‑1 (MQ=11)            ccGCGAACAACTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTACCAGTa                                  <  2:71506/50‑1 (MQ=11)             cgcgAACAACTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTACCAGTAc                                 <  1:1176646/50‑1 (MQ=11)              gcgAACAACTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTACCAGTAcc                                <  1:1080496/50‑1 (MQ=11)               cgAACAACTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTACCAGTACCg                               <  2:1255532/50‑1 (MQ=11)                 aacaacTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTACCAGTACCGa                              >  1:1499050/1‑49 (MQ=11)                  acaacTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTACCAGTACCGATa                            <  2:1557343/50‑1 (MQ=11)                     acTGAGTACCCCGTTCCGCTACGACATT‑CAGTTTACCAGTACCGATAAAg                         <  2:1803267/50‑1 (MQ=11)                         aGTACCCCGTTCCGCTACGACATT‑CAGTTTACCAGTACCGATAAAGcc                       <  2:606006/48‑1 (MQ=11)                         aGTACCCCGTTCCGCTACGACATT‑CAGTTTACCAGTACCGATAAAGcc                       <  1:430767/48‑1 (MQ=11)                         aGTACCCCGTTCCGCTACGACATT‑CAGTTTACCAGTACCGATAAAGcc                       <  1:1091250/48‑1 (MQ=11)                          gTACCCCGTTCCGCTACGACATT‑CAGTTTACCAGTACCGATAAAGCCATc                    <  1:107945/50‑1 (MQ=11)                          gTACCCCGTTCCGCTACGACATT‑CAGTTTACCAGTACCGATAAAGCCATc                    <  1:777809/50‑1 (MQ=11)                           tACCCCGTTCCGCTACGACATT‑CAGTTTACCAGTACCGATAAAGCCATCa                   <  1:1494022/50‑1 (MQ=11)                            aCCCCGTTCCGCTACGACATT‑CAGTTTACCAGTACCGATAAAGCCATCAc                  >  2:1197463/1‑50 (MQ=11)                            aCCCCGTTCCGCTACGACATT‑CAGTTTACCAGTACCGATAAAGCCATCAc                  >  1:732924/1‑50 (MQ=11)                            aCCCCGTTCCGCTACGACATT‑CAGTTTACCAGTACCGATAAAGCCATCAc                  >  1:1842823/1‑50 (MQ=11)                             ccccGTTCCGCTACGACATT‑CAGTTTACCAGTACCGATAAAGCCATCACg                 <  2:1770803/50‑1 (MQ=11)                             ccccGTTCCGCTACGACATT‑CAGTTTACCAGTACCGATAAAGCCATCACg                 <  2:203731/50‑1 (MQ=11)                             ccccGTTCCGCTACGACATT‑CAGTTTACCAGTACCGATAAAGCCATCACg                 <  2:384986/50‑1 (MQ=11)                                           gACATT‑CAGTTTACCAGTACCGATAAAGCCATCACGCCGGAGTTGGTGCt   <  1:1596497/50‑1 (MQ=11)                                            aCATT‑CAGTTTACCAGTACCGATAAAGCCATCACGCCGGAGTTGGTGCTg  <  2:1255392/50‑1 (MQ=1)                                                 |                                              ACCTTCGAAGGCCGCGAACAACTGAGTACCCCGTTCCGCTACGACATTCCAGTTTACCAGTACCGATAAAGCCATCACGCCGGAGTTGGTGCTG  >  NC_017635/3114835‑3114928

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑