Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,775,699	T→C	pseudogene (155/180 nt)	ypjI →	pseudogene, CP4‑57 putative prophage remnant;Phage or Prophage Related

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,775,699	0	T	C	100.0%	163.6 / NA	46	pseudogene (155/180 nt)	ypjI	pseudogene, CP4‑57 putative prophage remnant;Phage or Prophage Related
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (24/22);  total (24/22)

ACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGTCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGTTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAGGTTTTAACCGCTATATCCACAGGTCAGGCATCCGCACCGACACCTTCCCCCGCTGACTCCGAATCATTTACCAGCAACATTTCAC  >  NC_000913/2775552‑2775845                                                                                                                                                    |                                                                                                                                                   aCTATGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGTCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTc                                                                                                                                                  >  1:538115/1‑150 (MQ=255)    ctGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGTCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTg                                                                                                                                               >  1:216158/1‑150 (MQ=255)     tGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGTCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGAt                                                                                                                                             >  1:699444/1‑151 (MQ=255)             ggTAGTCATTTTAGCAAACGCTTTCTGGTCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAg                                                                                                                                      <  1:255651/150‑1 (MQ=255)              gTAGTCATTTTAGCAAACGCTTTCTGGTCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCCTTCACGTCCGCCTGATAGCTCGTGATGCCGAAg                                                                                                                                      <  1:805711/149‑1 (MQ=255)              gTAGTCATTTTAGCAAACGCTTTCTGGTCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGt                                                                                                                                    >  2:778766/1‑151 (MQ=255)                aGTCCTTTTAGCAAACGCTTTCTGGTCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCACCTGATAGCTCGTGATGCCGAAGGTCg                                                                                                                                  >  1:810428/1‑151 (MQ=255)                aGTCATTTTAGCAAACGCTTTCTGGTCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTc                                                                                                                                   <  2:608903/150‑1 (MQ=255)                   cATTTTAGCAAACGCTTTCTGGTCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGAt                                                                                                                               <  2:511530/151‑1 (MQ=255)                   cATTTTAGCAAACGCTTTCTGGTCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGAt                                                                                                                               <  2:49098/151‑1 (MQ=255)                        tAGCAAACGCTTTCTGGTCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGtt                                                                                                                           <  2:385984/150‑1 (MQ=255)                            aaaCGCTTTCTGGTCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCg                                                                                                                       >  2:246885/1‑150 (MQ=255)                              aCGCTTTCTGGTCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGc                                                                                                                    >  2:280896/1‑151 (MQ=255)                                      aggTCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCAGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGTGGGCATGGAACt                                                                                                            >  1:678795/2‑151 (MQ=255)                                       ggTCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAAc                                                                                                             <  2:801182/149‑1 (MQ=255)                                       ggTCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACtt                                                                                                           >  1:313407/1‑151 (MQ=255)                                       ggTCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACt                                                                                                            <  1:135618/150‑1 (MQ=255)                                            gCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAAc                                                                                                      >  1:613753/1‑151 (MQ=255)                                                   tGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGc                                                                                               >  2:158784/1‑151 (MQ=255)                                                        aTCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTg                                                                                          <  2:145112/151‑1 (MQ=255)                                                           ggCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAg                                                                                       <  1:77712/151‑1 (MQ=255)                                                                     gTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAGGTTTTAACCg                                                                             >  1:154561/1‑151 (MQ=255)                                                                          aGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAGGTTTTAACCGCtata                                                                        <  1:766851/151‑1 (MQ=255)                                                                          aGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAGGTTTTAACCGCtat                                                                         >  2:640460/1‑150 (MQ=255)                                                                                   ggTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAGGTTTTAACCGCTATATCCACAGGt                                                               >  1:435839/1‑151 (MQ=255)                                                                                      aTCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGACGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAGGTTTTAACCGCTATATCcac                                                                   >  2:85492/1‑144 (MQ=255)                                                                                          gCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAGGTTTTAACCGCTATATCCACAGGTCAGGc                                                          <  2:187593/149‑1 (MQ=255)                                                                                           ccGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAGGTTTTAACCGCTATATCCACAGGTCAGGCATc                                                       >  1:267617/1‑151 (MQ=255)                                                                                            cGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAGGTTTTAACCGCTATATCCACAGGTCAGGCATcc                                                      <  2:78260/151‑1 (MQ=255)                                                                                            cGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAGGTTTTAACCGCTATATCCACAGGTCAGGCATcc                                                      >  1:406868/1‑151 (MQ=255)                                                                                            cGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAGGTTTTAACCGCTATATCCACAGGTCAGGCATcc                                                      <  2:555878/151‑1 (MQ=255)                                                                                             ggTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAGGTTTTAACCGCTATATCCACAGGTCAGGCATc                                                       <  2:719209/149‑1 (MQ=255)                                                                                             ggTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAGGTTTTAACCGCTATATCCACAGGTCAGGCATCCg                                                     >  2:112551/1‑151 (MQ=255)                                                                                                aTCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAGGTTTTAACCGCTATATCCACAGGTCAGGCATCCGCAc                                                  >  2:747911/1‑151 (MQ=255)                                                                                                   aCCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAGGTTTTAACCGCTATATCCACAGGTCAGGCATCCGCACCGa                                               <  2:426530/151‑1 (MQ=255)                                                                                                    ccGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAGGTTTTAACCGCTATATCCACAGGTCAGGCATCCGCACCGac                                              >  1:130330/1‑151 (MQ=255)                                                                                                                    aGACGACCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGCCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGACGGTTTTAACCGCTATATCCACAGGTCAGGCATCCGCACCGACACCTTCCCCCGCTGAc                              >  1:353727/1‑151 (MQ=255)                                                                                                                       cgacCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAGGTTTTAACCGCTATATCCACAGGTCAGGCATCCGCACCGACACCTTCCCCCGCTGACTcc                           <  1:549391/151‑1 (MQ=255)                                                                                                                         acCAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAGGTTTTAACCGCTATATCCACAGGTCAGGCATCCGCACCGACACCTTCCCCCGCTGACTCCGa                         <  1:400786/151‑1 (MQ=255)                                                                                                                          ccAGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAGGTTTTAACCGCTATATCCACAGGTCAGGCATCCGCACCGACACCTTCCCCCGCTGACTCCGaa                        <  2:448000/151‑1 (MQ=255)                                                                                                                            aGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAGGTTTTAACCGCTATATCCACAGGTCAGGCATCCGCACCGACACCTTCCCCCGCTGACTCCGAATc                      <  2:588588/151‑1 (MQ=255)                                                                                                                            aGGGCATTCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAGGTTTTAACCGCTATATCCACAGGTCAGGCATCCGCACCGACACCTTCCCCCGCTGACTCCGAATc                      <  1:766400/151‑1 (MQ=255)                                                                                                                                  ttCACGTCCGCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAGGTTTTAACCGCTATATCCACAGGTCAGGCATCCGCACCGACACCTTCCCCCGCTGACTCCGAATCATTTAc                >  1:36521/1‑151 (MQ=255)                                                                                                                                           gCCTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAGGTTTTAACCGCTATATCCACAGGTCAGGCATCCGCACCGACACCTTCCCCCGCTGACTCCGAATCATTTACCAGCAACAt       >  1:237814/1‑151 (MQ=255)                                                                                                                                             cTGATAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAGGTTTTAACCGCTATATCCACAGGTCAGGCATCCGCACCGACACCTTCCCCCGCTGACTCCGAATCATTTACCAGCAACAttt     >  2:600085/1‑151 (MQ=255)                                                                                                                                                aTAGCTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAGGTTTTAACCGCTATATCCACAGGTCAGGCATCCGCACCGACACCTTCCCCCGCTGACTCCGAATCATTTACCAGCAACATTTCAc  <  2:237838/151‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                   ACTCTGAAGGTTGGTAGTCATTTTAGCAAACGCTTTCTGGTCTGCCGCAGTGGGCATCGGCTGATTGCGTAGCAGGGCCACTGGTATCTGCCGGTATCACCGACATTAACATTGAAGACGACCAGGGCATTCACGTCCGCCTGATAGTTCGTGATGCCGAAGGTCGGATGGTTGGCGGGCATGGAACTTTGAACCGGACGCCGGTGAAGGTTTTAACCGCTATATCCACAGGTCAGGCATCCGCACCGACACCTTCCCCCGCTGACTCCGAATCATTTACCAGCAACATTTCAC  >  NC_000913/2775552‑2775845

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑