Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,433,718	T→C	intergenic (‑44/+273)	pinR ← / ← ynaE	Rac prophage; putative site‑specific recombinase/cold shock protein, Rac prophage

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,433,718	0	T	C	100.0%	171.1 / NA	76	intergenic (‑44/+273)	pinR/ynaE	Rac prophage; putative site‑specific recombinase/cold shock protein, Rac prophage
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (34/42);  total (34/42)

TTCGGTGGTCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGT  >  NC_000913/1433621‑1433764                                                                                                  |                                               tcttccgatCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCa                                              <  1:2321716/92‑1 (MQ=11)  tCGGTGGTCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAg                                             <  1:2172142/100‑1 (MQ=17)    ggtggtCTGCTCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGGCATAGTGAGACTCTATACGAAAATGGTGTTCATATCATACTGCATCCCCGaa                                           >  1:2232555/1‑100 (MQ=11)    ggtggtCTGATCCAGCGTTGATATCAGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGaa                                           <  1:1755304/100‑1 (MQ=255)     gttgtCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGaaa                                          <  1:1028600/97‑1 (MQ=12)     gttgtCTAATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAATGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGaaa                                          <  1:2966641/97‑1 (MQ=11)     gtggtCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGaaa                                          >  1:2793019/1‑100 (MQ=18)      tggtCTGATCCAGCTTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGaaaa                                         <  2:286360/100‑1 (MQ=12)       ggtCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAaat                                        >  2:3392957/1‑100 (MQ=18)       ggtCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAaat                                        >  2:1272022/1‑100 (MQ=18)        gtCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAaata                                       >  1:2615413/1‑100 (MQ=18)         tCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAaataa                                      <  1:1432810/100‑1 (MQ=18)         tCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAaataa                                      >  2:1432831/1‑100 (MQ=18)         tCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAaataa                                      >  1:1239546/1‑100 (MQ=18)         tCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAaataa                                      >  1:1238545/1‑100 (MQ=18)         tCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAaataa                                      >  1:1815423/1‑100 (MQ=18)          cTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAaataat                                     >  1:2821288/1‑100 (MQ=18)           tGATCCAGTGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAAtt                                    <  2:1153508/100‑1 (MQ=16)           tGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAAtt                                    >  1:1101245/1‑100 (MQ=18)           tGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAAtt                                    >  1:1838638/1‑100 (MQ=18)           tGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAAtt                                    <  2:59427/100‑1 (MQ=17)            gATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTa                                   >  1:504953/1‑100 (MQ=18)            gATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTa                                   <  2:478299/100‑1 (MQ=18)            gATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACCCTATAAGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAAtt                                    >  2:1098452/1‑99 (MQ=255)             aTCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTAt                                  >  1:3284141/1‑100 (MQ=18)             aTCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTAt                                  >  1:1815961/1‑100 (MQ=18)               ccAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGa                                >  2:1302049/1‑100 (MQ=18)                cAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATACCATAATGCATCCCAGAAAATAATTATGat                               >  1:2091027/1‑100 (MQ=16)                 aGCGTTGATATCCGACAGTAAGCAAAAATTCTAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAaataat                                     <  1:2284207/93‑1 (MQ=12)                  gCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATTCCAGAAAATAATTATGatta                             <  1:2129215/100‑1 (MQ=255)                  gCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGatta                             >  2:2481656/1‑100 (MQ=18)                   cGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGattat                            >  2:836879/1‑100 (MQ=18)                    gTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGTGACTCTAGACGATATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGa                                <  1:2194161/95‑1 (MQ=11)                       gATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTAttttt                        >  2:1988848/1‑100 (MQ=17)                        atatCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTtg                       <  1:3193561/100‑1 (MQ=17)                        atatCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTtg                       <  2:1690054/100‑1 (MQ=18)                        atatCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTtg                       >  1:348665/1‑100 (MQ=18)                        atatCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTtg                       <  2:1809414/100‑1 (MQ=17)                         tatCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTtgt                      >  2:282204/1‑100 (MQ=17)                         tatCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATCACAATTAttttctg                      <  2:2288063/100‑4 (MQ=11)                          attcGACAGTAAGCAAAAATTCGGTACATAGTGAGACTCTATACGAAATTGGTGTTAATATCATAATGCAGCCCAGAAAATAATCATAATTAttttctgg                     <  1:531967/97‑5 (MQ=11)                          atCCGACAGTAAGTAAAAATTCGAGACATAGTGAGACTCTAAACGATATTGGTATTCATATCATAATGCATCCCAGAAAATAATCATAATTAttttctgg                     <  1:1559473/100‑5 (MQ=11)                          atCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTtgtg                     <  2:3320163/100‑1 (MQ=18)                           tCCGACAGTAAGCAAATATTCGAGACATAGTGAGACTCTATACGAAATTGGTATTCATATCATAATGCATCCCAGAAAATAATCATAATTAttttctgg                     <  1:1516451/99‑5 (MQ=11)                           tCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCTTCCCAGAAAATAATCATTATTAttttctgtg                    <  2:2342155/100‑6 (MQ=11)                            ccGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCa                   <  2:640234/100‑1 (MQ=18)                             cGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCat                  <  1:1302030/100‑1 (MQ=18)                             cGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCat                  >  1:1544089/1‑100 (MQ=18)                             cGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCat                  >  1:1787803/1‑100 (MQ=18)                             cGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCat                  >  1:3272541/1‑100 (MQ=18)                             cGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCat                  >  1:1234188/1‑100 (MQ=18)                             cGAAAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCTTAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCat                  <  1:2783784/100‑1 (MQ=255)                              gACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCata                 >  2:533096/1‑100 (MQ=18)                                  gTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTtg             <  1:1643095/100‑1 (MQ=17)                                  gTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTtg             <  2:1160632/100‑1 (MQ=18)                                  gTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTtg             <  1:290630/100‑1 (MQ=17)                                  gTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTCTGTGCATATTtg             <  2:2279955/100‑1 (MQ=255)                                   tAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTtgt            <  1:3023224/100‑1 (MQ=17)                                    aaGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTtgta           <  2:3272592/100‑1 (MQ=18)                                    aaGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTtgta           <  2:2629517/100‑1 (MQ=18)                                    aaGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTtgta           <  1:2239430/100‑1 (MQ=18)                                    aaGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTtgta           <  2:1838663/100‑1 (MQ=18)                                     aGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTTATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTtgta           <  1:2878333/99‑1 (MQ=12)                                      gCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTtgtatg         <  2:2103491/100‑1 (MQ=18)                                      gCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTtgtatg         <  2:196435/100‑1 (MQ=18)                                      gCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTtgtatg         >  2:838640/1‑100 (MQ=17)                                       cAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTtgtatgt        >  2:2207659/1‑100 (MQ=18)                                       cAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTtgtatgt        >  1:943788/1‑100 (MQ=18)                                         aaaaTTCGAGAGATAGTGAGACTCTATACGAAATTGGTGTTCATATTATAATGCATCCCAGAAAATAATTATGATTATTTTTTTGCATATTTGTATGTac      <  1:1332570/100‑1 (MQ=11)                                         aaaaTTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTac      >  1:1572486/1‑100 (MQ=18)                                         aaaaTTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTac      >  1:3200485/1‑100 (MQ=18)                                          aaaTTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTaca     <  2:2502670/100‑1 (MQ=18)                                          aaaTTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTaca     <  2:1797585/100‑1 (MQ=18)                                           aaTTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATTCCAGAAAATAATTATGATTATTTTTGTGCATATTtgtatgn        <  1:708821/96‑2 (MQ=12)                                            aTTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACg   <  1:2737268/100‑1 (MQ=17)                                             ttCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGt  >  2:876585/1‑100 (MQ=17)                                                                                                  |                                               TTCGGTGGTCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGT  >  NC_000913/1433621‑1433764

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑