Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,381,789	G→A	pseudogene (13/126 nt)	ycjV →	pseudogene, putative ATP‑binding component of a transport system

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,381,789	0	G	A	100.0%	133.2 / NA	42	pseudogene (13/126 nt)	ycjV	pseudogene, putative ATP‑binding component of a transport system
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (22/20);  total (22/20)

ATCGTGATGGGAATACGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAGTGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAGGGGGAAGGCAT  >  NC_000913/1381655‑1381919                                                                                                                                       |                                                                                                                                   aTCGTGATGGGAATACGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGt                                                                                                                                <  2:619286/139‑1 (MQ=255)  tCGTGATGGGAATACGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTc                                                                                                                               >  1:1348084/1‑139 (MQ=255)        tGGGAATACGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCt                                                                                                                         >  1:133384/1‑139 (MQ=255)           gAATACGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGt                                                                                                                      <  2:1348084/139‑1 (MQ=255)              tACGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCg                                                                                                                   <  1:282282/139‑1 (MQ=255)               aCGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGt                                                                                                                  <  1:1334193/139‑1 (MQ=255)                    cGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAAt                                                                                                             >  1:1076964/1‑139 (MQ=255)                      gAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGa                                                                                                           >  2:26642/1‑139 (MQ=255)                              tCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATg                                                                                                   <  1:26642/139‑1 (MQ=255)                                 tCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAg                                                                                                >  2:637640/1‑139 (MQ=255)                                                 gAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGt                                                                                                                      >  2:585403/1‑101 (MQ=255)                                                 gAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGt                                                                                                                      <  1:585403/101‑1 (MQ=255)                                                            ttCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGata                                                                     >  1:1360565/1‑139 (MQ=255)                                                             tCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCg                                                                                                                             >  1:994461/1‑82 (MQ=255)                                                             tCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTATACACTACGGTTGGGGGCACGAGTTAATGGTCCg                                                                                                                             <  2:994461/82‑1 (MQ=255)                                                              ccGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATg                                                                   >  2:425514/1‑139 (MQ=255)                                                                gCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGAc                                                                 >  1:1392956/1‑139 (MQ=255)                                                                           cGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTg                                                                                                                        <  1:1035298/73‑1 (MQ=255)                                                                           cGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTg                                                                                                                        >  2:1035298/1‑73 (MQ=255)                                                                               gCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTg                                                                                                                           >  2:1501622/1‑66 (MQ=255)                                                                               gCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTg                                                                                                                           <  1:1501622/66‑1 (MQ=255)                                                                               gCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCtt                                                  <  2:1076964/139‑1 (MQ=255)                                                                                           ggTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGGGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAAc                                      <  2:1360565/139‑1 (MQ=255)                                                                                                       aTGCTCTACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAAt                          <  2:1392956/139‑1 (MQ=255)                                                                                                            ctACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTa                                                                                                                <  1:862200/48‑1 (MQ=255)                                                                                                            ctACACCACGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGGGCGTTa                                                                                                                >  2:862200/1‑48 (MQ=255)                                                                                                                 ccacGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAg                                                                                                >  1:335013/1‑59 (MQ=255)                                                                                                                 ccacGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAg                                                                                                <  2:335013/59‑1 (MQ=255)                                                                                                                  cacGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGc                                                                                                  <  2:671891/56‑1 (MQ=255)                                                                                                                  cacGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGc                                                                                                  >  1:671891/1‑56 (MQ=255)                                                                                                                  cacGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATAc               >  2:1190957/1‑139 (MQ=255)                                                                                                                    cGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAAt                          >  1:425939/1‑126 (MQ=255)                                                                                                                    cGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAAt                          <  2:425939/126‑1 (MQ=255)                                                                                                                    cGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAg             >  2:166149/1‑139 (MQ=255)                                                                                                                    cGGTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAg             >  2:61742/1‑139 (MQ=255)                                                                                                                     ggTTGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAgg            >  1:1453240/1‑139 (MQ=255)                                                                                                                       ttGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAgggg          >  2:806101/1‑139 (MQ=255)                                                                                                                        tGGGGGCACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAggggg         <  2:1453240/139‑1 (MQ=255)                                                                                                                         gggggCACGAGTTAATGGTCCGTGCTGGTGCGTTaa                                                                                                               >  1:1398123/1‑36 (MQ=255)                                                                                                                         gggggCACGAGTTAATGGTCCGTGCTGGTGCGTTaa                                                                                                               <  2:1398123/36‑1 (MQ=255)                                                                                                                              cACGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAGATACAGGGGGAAGGCa   <  1:637640/139‑1 (MQ=255)                                                                                                                               aCGAGTTAATGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAGGGGGAAGGCAt  <  1:61742/139‑1 (MQ=255)                                                                                                                                       |                                                                                                                                   ATCGTGATGGGAATACGACCGGAAGATATTCATCCGGACGCGCAAGAGGAAAATAACATTTCCGCCAAAATTAGCGTGGCAGAATTAACCGGTGCGGAATTTATGCTCTACACCACGGTTGGGGGCACGAGTTAGTGGTCCGTGCTGGTGCGTTAAATGATTATCATGCAGGAGAAAATATCACTATTCATTTTGATATGACGAAATGTCATTTCTTTGATGCAGAAACGGAAATAGCAATTCGCTAAATACAGGGGGAAGGCAT  >  NC_000913/1381655‑1381919

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑