Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,204,591	A→G	N141S (AAC→AGC)  pseudogene (191/1137 nt)	ymfN → aaaE →	e14 prophage; chimeric replication protein/phage terminase YmfN phage terminase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,204,591	0	A	G	100.0%	117.0 / NA	34	N141S (AAC→AGC)  pseudogene (191/1137 nt)	ymfN aaaE	e14 prophage; chimeric replication protein/phage terminase YmfN phage terminase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (13/21);  total (13/21)

GGCCATTACCACCGCCGGGTACAACATTGAGGGGCCGTGCTACGACAAACGGCGGGAAGTCATCGAGATGCTCAACGGCTCGGTGCCAAACGATGAACTGTTCGGGATCATCTATACCGTTGATGAAGGTGACGACTGGACCGACCCGCAG  >  NC_000913/1204517‑1204667                                                                           |                                                                             ggCCATTACCACCGCCGGGTACAACATTGAGGGGCCGTGCTACGACAAACGGCGGGAAGTCATCGAGATGCTCAGCGGCt                                                                         <  2:238257/80‑1 (MQ=255) ggCCATTACCACCGCCGGGTACAACATTGAGGGGCCGTGCTACGACAAACGGCGGGAAGTCATCGAGATGCTCAGCGGCTc                                                                        >  2:238308/1‑81 (MQ=255) ggCCATTACCACCGCCGGGTACAACATTGAGGGGCCGTGCTACGACAAACGGCGGGAAGTCATCGAGATGCTCAGCGGCTc                                                                        <  1:238258/81‑1 (MQ=255)  gCCATTACCACCGCCGGGTACAACATTGAGGGGCCGTGCTACGACAAACGGCGGGAAGTCATCGAGATGCTCAGCGGCTCg                                                                       <  1:238259/81‑1 (MQ=255)    cATTACCACCGCCGGGTACAACATTGAGGGGCCGTGCTACGACAAACGGCGGGAAGTCATCGAGATGCTCAGCGGCTCGGt                                                                     <  2:238260/81‑1 (MQ=255)        accaccGCCGGGTACAACATTGAGGGGCCGTGCTACGACAAACGGCGGGAAGTCATCGAGATGCTCAGCGGCTCGGTGcc                                                                  >  2:238301/1‑80 (MQ=255)           accGCCGGGTACAACATTGAGGGGCCGTGCTACGACAAACGGCGGGAAGTCATCGAGATGCTCAGCGGCTCGGTGCCAAAc                                                              <  1:238261/81‑1 (MQ=255)            ccgccgGGTACAACATTGAGGGGCCGTGCTACGACAAACGGCGGGAAGTCATCGAGATGCTCAGCGGCTCGGTGCCAAACg                                                             <  2:238262/81‑1 (MQ=255)             cgccgGGTACAACATTGAGGGGCCGTGCTACGACAAACGGCGGGAAGTCATCGAGATGCTCAGCGGCTCGGTGCCAAACGa                                                            <  1:238263/81‑1 (MQ=255)                      caacaTTGAGGGGCCGTGCTACGACAAACGGCGGGAAGTCATCGAGATGCTCAGCGGCTCGGTGCCAAACGATGAACTGt                                                    <  1:238264/80‑1 (MQ=255)                         caTTGAGGGGCCGTGCTACGACAAACGGCGGGAAGTCATCGAGATGCTCAGCGGCTCGGTGCCAAACGATGAACTGTTCgg                                                >  2:238306/1‑81 (MQ=255)                           ttGAGGGGCCGTGCTACGACAAACGGCGGGAAGTCATCGAGATGCTCAGCGGCTCGGTGCCAAACGATGAACTGTTCGGGa                                              <  2:238265/81‑1 (MQ=255)                             gAGGGGCCGTGCTACGACAAACGGCGGGAAGTCATCGAGATGCTCAGCGGCTCGGTGCCAAACGATGAACTGTTCGGGat                                             >  2:238309/1‑80 (MQ=255)                              aGGGGCCGTGCTACGACAAACGGCGGGAAGTCATCGAGATGCTCAGCGGCTCGGTGCCAAACGATGAACTGTTCGGGatc                                            <  1:238266/80‑1 (MQ=255)                               ggggCCGTGCTACGACAAACGGCGGGAAGTCATCGAGATGCTCAGCGGCTCGGTGCCAAACGATGAACTGTTCGGGatcat                                          >  2:238296/1‑81 (MQ=255)                                gggCCGTGCTACGACAAACGGCGGGAAGTCATCGAGATGCTCAGCGGCTCGGTGCCAAACGATGAACTGTTCGGGatcatc                                         >  2:238302/1‑81 (MQ=255)                                 ggCCGTGCTACGACAAACGGCGGGAAGTCATCGAGATGCTCAGCGGCTCGGTGCCAAACGATGAACTGTTCGGGatcatc                                         >  2:238289/1‑80 (MQ=255)                                     gTGCTACGACAAACGGCGGGAAGTCATCGAGATGCTCAGCGGCTCGGTGCCAAACGATGAACTGTTCGGGATCATCTATAc                                    <  1:238267/81‑1 (MQ=255)                                      tGCTACGACAAACGGCGGGAAGTCATCGAGATGCTCAGCGGCTCGGTGCCAAACGATGAACTGTTCGGGATCATCTATAcc                                   <  1:238268/81‑1 (MQ=255)                                      tGCTACGACAAACGGCGGGAAGTCATCGAGATGCTCAGCGGCTCGGTGCCAAACGATGAACTGTTCGGGATCATCTATAcc                                   >  2:238305/1‑81 (MQ=255)                                           cGACAAACGGCGGGAAGTCATCGAGATGCTCAGCGGCTCGGTGCCAAACGATGAACTGTTCGGGATCATCTATACCGTtg                               <  2:238269/80‑1 (MQ=255)                                            gACAAACGGCGGGAAGTCATCGAGATGCTCAGCGGCTCGGTGCCAAACGATGAACTGTTCGGGATCATCTATACCGTtgat                             >  2:238314/1‑81 (MQ=255)                                            gACAAACGGCGGGAAGTCATCGAGATGCTCAGCGGCTCGGTGCCAAACGATGAACTGTTCGGGATCATCTATACCGTtgat                             >  2:238312/1‑81 (MQ=255)                                               aaaCGGCGGGAAGTCATCGAGATGCTCAGCGGCTCGGTGCCAAACGATGAACTGTTCGGGATCATCTATACCGTTGATGaa                          <  1:238270/81‑1 (MQ=255)                                                aaCGGCGGGAAGTCATCGAGATGCTCAGCGGCTCGGTGCGAAACGATGAACTGTTCGGGATAATCTATACCGTTGATGAAg                         <  2:238271/81‑1 (MQ=255)                                                   ggcggGAAGTCATCGAGATGCTCAGCGGCTCGGTGCCAAACGATGAACTGTTCGGGATCATCTATACCGTTGATGAAGGTg                      <  2:238272/81‑1 (MQ=255)                                                      gggAAGTCATCGAGATGCTCAGCGGCTCGGTGCCAAACGATGAACTGTTCGGGATCATCTATACCGTTGATGAAGGTgac                    >  1:238298/1‑80 (MQ=255)                                                       ggAAGTCATCGAGATGCTCAGCGGCTCGGTGCCAAACGATGAACTGTTCGGGATCATCTATACCGTTGATGAAGGTgacga                  >  2:238304/1‑81 (MQ=255)                                                           gTCATCGAGATGCTCAGCGGCTCGGTGCCAAACGATGAACTGTTCGGGATCATCTATACCGTTGATGAAGGTGACGACTgg              <  2:238273/81‑1 (MQ=255)                                                             cATCGAGATGCTCAGCGGCTCGGTGCCAAACGATGAACTGTTCGGGATCATCTATACCGTTGATGAAGGTGACGACTGgac            >  2:238300/1‑81 (MQ=255)                                                              aTCGAGATGCTCAGCGGCTCGGTGCCAAACGATGAACTGTTCGGGATCATCTATACCGTTGATGAAGGTGACGACTGgac            <  1:238274/80‑1 (MQ=255)                                                               tCGAGATGCTCAGCGGCTCGGTGCCAAACGATGAACTGTTCGGGATCATCTATACCGTTGATGAAGGTGACGACTGgaccg          <  2:238275/81‑1 (MQ=255)                                                                       cTCAGCGGCTCGGTGCCAAACGATGAACTGTTCGGGATCATCTATACCGTTGATGAAGGTGACGACTGGACCGACCCGCa   <  1:238276/80‑1 (MQ=255)                                                                       cTCAGCGGCTCGGTGCCAAACGATGAACTGTTCGGGATCATCTATACCGTTGATGAAGGTGACGACTGGACCGACCCGCAg  <  2:238277/81‑1 (MQ=255)                                                                           |                                                                             GGCCATTACCACCGCCGGGTACAACATTGAGGGGCCGTGCTACGACAAACGGCGGGAAGTCATCGAGATGCTCAACGGCTCGGTGCCAAACGATGAACTGTTCGGGATCATCTATACCGTTGATGAAGGTGACGACTGGACCGACCCGCAG  >  NC_000913/1204517‑1204667

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑