Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,632,369	T→C	intergenic (‑84/‑703)	ydfJ ← / → ydfK	pseudogene, MFS transporter family; interrupted by Qin prophage;Phage or Prophage Related; putative transport protein/cold shock protein, function unknown, Qin prophage

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,632,369	0	T	C	100.0%	211.3 / NA	55	intergenic (‑84/‑703)	ydfJ/ydfK	pseudogene, MFS transporter family; interrupted by Qin prophage;Phage or Prophage Related; putative transport protein/cold shock protein, function unknown, Qin prophage
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (38/17);  total (38/17)

GGAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTGGAAATCATTCAATACTCACACT  >  NC_000913/1632227‑1632510                                                                                                                                               |                                                                                                                                              ggAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGtt                                                                                                                                       <  2:524520/151‑1 (MQ=255) ggAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGtt                                                                                                                                       <  2:153900/151‑1 (MQ=255)  gAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTc                                                                                                                                      >  2:724799/1‑151 (MQ=255)    aaaaaTATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCg                                                                                                                                     >  2:50786/1‑150 (MQ=255)        atatTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGAtctc                                                                                                                                >  1:91679/1‑151 (MQ=255)                tGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCt                                                                                                                         >  2:39104/1‑150 (MQ=255)                tGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCt                                                                                                                         >  1:765392/1‑150 (MQ=255)                 gAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTAt                                                                                                                       >  2:242989/1‑151 (MQ=255)                   aaCACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCt                                                                                                                     >  1:228965/1‑151 (MQ=255)                    acacTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTg                                                                                                                    <  1:724725/151‑1 (MQ=255)                        tAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGc                                                                                                                >  2:213105/1‑151 (MQ=255)                        tAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGc                                                                                                                >  2:322567/1‑151 (MQ=255)                         aaCGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGcc                                                                                                               >  1:160318/1‑151 (MQ=255)                           cGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCt                                                                                                              >  1:441315/1‑150 (MQ=255)                                cgcCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCt                                                                                                        <  1:529807/151‑1 (MQ=255)                                    gAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTcc                                                                                                    >  1:758448/1‑151 (MQ=255)                                     aGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTccc                                                                                                   >  1:733962/1‑151 (MQ=255)                                              aaCTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGcc                                                                                          <  2:627399/151‑1 (MQ=255)                                                 tGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGcccc                                                                                        >  1:562676/1‑150 (MQ=255)                                                  ggAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCa                                                                                       <  1:77430/150‑1 (MQ=255)                                                     aaTCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCaaaa                                                                                    >  1:573300/1‑150 (MQ=255)                                                      aTCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCaaaaa                                                                                   >  2:434431/1‑150 (MQ=255)                                                        ccATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAAc                                                                                <  2:91710/151‑1 (MQ=255)                                                         cATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACt                                                                               >  1:252809/1‑151 (MQ=255)                                                          aTAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTc                                                                              >  1:486578/1‑151 (MQ=255)                                                            aaTTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTccc                                                                            >  1:429569/1‑151 (MQ=255)                                                                cacaGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAAc                                                                        >  2:528780/1‑151 (MQ=255)                                                                cacaGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAAc                                                                        >  2:144344/1‑151 (MQ=255)                                                                           tttCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAagtagt                                                             >  2:8876/1‑151 (MQ=255)                                                                             tCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGttt                                                           >  1:488722/1‑151 (MQ=255)                                                                              cccATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGttt                                                           <  1:43409/150‑1 (MQ=255)                                                                              cccATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGttt                                                           <  2:411955/150‑1 (MQ=255)                                                                                cATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGtttttt                                                        <  1:518895/151‑1 (MQ=255)                                                                                cATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGtttttt                                                        <  1:688806/151‑1 (MQ=255)                                                                                   ccTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCAt                                                     >  1:538569/1‑151 (MQ=255)                                                                                        ggTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGAtt                                                <  2:676754/151‑1 (MQ=255)                                                                                             ccTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGc                                           <  2:228121/151‑1 (MQ=255)                                                                                                    gTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAAt                                    >  1:76964/1‑151 (MQ=255)                                                                                                    gTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAAt                                    >  1:470412/1‑151 (MQ=255)                                                                                                      tttCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATc                                   <  1:727914/150‑1 (MQ=255)                                                                                                                  ttCAGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTgg                       >  1:231144/1‑150 (MQ=255)                                                                                                                     aGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTGGAAAt                   >  1:465651/1‑151 (MQ=255)                                                                                                                     aGATAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTGGAAAt                   <  1:22399/151‑1 (MQ=255)                                                                                                                       aTAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTGGAAATc                  >  1:568963/1‑150 (MQ=255)                                                                                                                       aTAGTTGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTGGAAATCa                 <  1:213073/151‑1 (MQ=255)                                                                                                                         aGTTGCATTTTTTT‑AAAAGCACCCTAAGTTCGATCTCAGGGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGGAAAATCAAGAACGGCTGGAAATCAtt               >  1:319922/1‑150 (MQ=255)                                                                                                                            tGCATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTGGAAATCATTCa             >  1:195891/1‑150 (MQ=255)                                                                                                                              cATTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTGGAAATCATTCAAt           >  2:259684/1‑150 (MQ=255)                                                                                                                               aTTTTTTTAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTGGAAATCATTCAATAc         <  2:455110/151‑1 (MQ=255)                                                                                                                                 ttttttAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTGGAAATCATTCAATACTc       >  2:99545/1‑151 (MQ=255)                                                                                                                                    tttAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTGGAAATCATTCAATACTcac     >  2:302207/1‑150 (MQ=255)                                                                                                                                     ttAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTGGAAATCATTCAATACTCacac   >  2:585651/1‑151 (MQ=255)                                                                                                                                      tAAAAAGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTGGAAATCATTCAATACTCACACt  >  2:61480/1‑151 (MQ=255)                                                                                                                                       aaaaaGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTGGAAATCATTCAATACTCACACt  >  2:762984/1‑150 (MQ=255)                                                                                                                                       aaaaaGCACCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGAATTATGCGTAAAATCAAGAACGGCTGGAAATCATTCAATACTCACACt  >  2:603792/1‑150 (MQ=255)                                                                                                                                               |                                                                                                                                              GGAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCATGGATTTATGCGTAAAATCAAGAACGGCTGGAAATCATTCAATACTCACACT  >  NC_000913/1632227‑1632510

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑