Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,650,536	G→T	pseudogene (459/921 nt)	ydfE →	Qin prophage; protein YdfE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,650,536	0	G	T	100.0%	194.5 / NA	55	pseudogene (459/921 nt)	ydfE	Qin prophage; protein YdfE
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (26/29);  total (26/29)

CTGGCCCCTGAAGTACAGAACGCTGTCATGGTTAAGTTCGACACATGTGAAAACATCACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCGTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAATTCAGGCAGAGATGCGCATCTGGAAAAAACG  >  NC_000913/1650402‑1650670                                                                                                                                       |                                                                                                                                       cTGGCCCCTGAAGTACAGAACGCTGTCATGGTTAAGTTCGACACATGTGAAAACATCACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTtgat                                                                                                                                   >  2:171031/1‑140 (MQ=255)    gCCCCTGAAGTACAGAACGCTGTCATGGTTAAGTTCGACACATGTGAAAACATCACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGaa                                                                                                                                <  2:86602/140‑1 (MQ=255)                cAGAACGCTGTCATGGTTAAGTTCGACACATGTGAAAACATCACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGt                                                                                                                    >  2:22055/1‑140 (MQ=255)                cAGAACGCTGTCATGGTTAAGTTCGACACATGTGAAAACATCACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGt                                                                                                                    <  1:775154/140‑1 (MQ=255)                  gAACGCTGTCATGGTTAAGTTCGACACATGTGAAAACATCACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTa                                                                                                                  <  1:171031/140‑1 (MQ=255)                     cGCTGTCATGGTTAAGTTCGACACATGTGAAAACATCACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACg                                                                                                               >  1:565649/1‑140 (MQ=255)                        tGTCATGGTTAAGTTCGACACATGTGAAAACATCACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCa                                                                                                            >  2:131702/1‑140 (MQ=255)                        tGTCATGGTTAAGTTCGACACATGTGAAAACATCACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCa                                                                                                            >  2:518654/1‑140 (MQ=255)                        tGTCATGGTTAAGTTCGACACATGTGAAAACATCACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCa                                                                                                            >  1:209343/1‑140 (MQ=255)                              ggTTAAGTTCGACACATGTGAAAACATCACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATc                                                                                                      <  1:586065/140‑1 (MQ=255)                               gTTAAGTTCGACACATGTGAAAACATCACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATcc                                                                                                     >  1:140739/1‑140 (MQ=255)                                  aaGTTCGACACATGTGAAAACATCACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGa                                                                                                  >  2:372196/1‑140 (MQ=255)                                    gTTCGACACATGTGAAAACATCACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGc                                                                                                >  2:75792/1‑140 (MQ=255)                                       cGACACATGTGAAAACATCACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTa                                                                                             <  1:75792/140‑1 (MQ=255)                                         acacATGTGAAAACATCACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAg                                                                                           >  1:114390/1‑140 (MQ=255)                                              tgtgAAAACATCACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGTCATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCa                                                                                      <  2:703452/140‑1 (MQ=255)                                               gtgAAAACATCACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCAc                                                                                     >  2:101681/1‑140 (MQ=255)                                                    aaCATCACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAg                                                                                           >  1:550421/1‑129 (MQ=255)                                                    aaCATCACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAg                                                                                           <  2:550421/129‑1 (MQ=255)                                                       aTCACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATtgg                                                                             <  2:423243/140‑1 (MQ=255)                                                        tCACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATtggg                                                                            <  2:565649/140‑1 (MQ=255)                                                         cACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATtgggt                                                                           <  1:586068/140‑1 (MQ=255)                                                         cACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATtgggt                                                                           >  1:72037/1‑140 (MQ=255)                                                         cACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATtgggt                                                                           >  2:22834/1‑140 (MQ=255)                                                         cACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATtgggt                                                                           <  2:140739/140‑1 (MQ=255)                                                            cGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCa                                                                                      >  1:705720/1‑126 (MQ=255)                                                            cGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCa                                                                                      <  2:705720/126‑1 (MQ=255)                                                              ttGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGtt                                                                      <  1:120867/140‑1 (MQ=255)                                                                 atatGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAg                                                                   >  2:126765/1‑140 (MQ=255)                                                                   atGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCa                                                                 <  1:743626/140‑1 (MQ=255)                                                                    tGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCAt                                                                <  2:456070/140‑1 (MQ=255)                                                                    tGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCAt                                                                <  1:131702/140‑1 (MQ=255)                                                                         attaGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATtggg                                                                            >  2:333047/1‑123 (MQ=255)                                                                         attaGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATtggg                                                                            <  1:333047/123‑1 (MQ=255)                                                                           taGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTa                                                         <  2:226866/140‑1 (MQ=255)                                                                            aGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTAt                                                        >  2:155365/1‑140 (MQ=255)                                                                              cgcACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTc                                                      >  2:199724/1‑140 (MQ=255)                                                                               gcACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTcc                                                     <  1:101681/140‑1 (MQ=255)                                                                               gcACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTcc                                                     <  2:576363/140‑1 (MQ=255)                                                                               gcACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTcc                                                     <  1:625009/140‑1 (MQ=255)                                                                                cacaGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCt                                                    >  2:328801/1‑140 (MQ=255)                                                                                cacaGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCt                                                    >  2:405598/1‑140 (MQ=255)                                                                                   aGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCa                                                                 >  1:334425/1‑124 (MQ=255)                                                                                   aGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCa                                                                 <  2:334425/124‑1 (MQ=255)                                                                                   aGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGt                                                 >  1:711676/1‑140 (MQ=255)                                                                                        ttgttgCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTaa                                            <  1:405598/140‑1 (MQ=255)                                                                                         tgttgCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTaaa                                           <  1:199724/140‑1 (MQ=255)                                                                                             gCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGc                                       >  2:75461/1‑140 (MQ=255)                                                                                               aGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGccc                                     <  1:22055/140‑1 (MQ=255)                                                                                                    gACATGGCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAAt                                <  1:372196/140‑1 (MQ=255)                                                                                                         ggCAACATTCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAATTCAgg                           <  2:711676/140‑1 (MQ=255)                                                                                                                 tCGACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAATTCAGGCAGAGATg                   <  1:75461/140‑1 (MQ=255)                                                                                                                   gACGGACATATCGTTGAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAATTCAGGCAGAGATgcg                 <  2:209343/140‑1 (MQ=255)                                                                                                                                  gAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAATTCAGGCAGAGATGCGCATCTGGAAAAAACg  >  2:222299/1‑140 (MQ=255)                                                                                                                                  gAAGCTTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAATTCAGGCAGAGATGCGCATCTAGAAAAAACg  >  2:28454/1‑140 (MQ=255)                                                                                                                                       |                                                                                                                                       CTGGCCCCTGAAGTACAGAACGCTGTCATGGTTAAGTTCGACACATGTGAAAACATCACCGTTGATATGGTTATTAGCGCACAGGAATTGTTGCAGGAAGACATGGCAACATTCGACGGACATATCGTTGAAGCGTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAATTCAGGCAGAGATGCGCATCTGGAAAAAACG  >  NC_000913/1650402‑1650670

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑