Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,433,718	T→C	100%	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%	87.6 / ‑6.7	44	intergenic (‑44/+273)	pinR/ynaE	Rac prophage; putative site‑specific recombinase/cold shock protein, Rac prophage
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (28/15);  total (28/16)

GTGGTCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGAAAATAAACGAATGCGTATGCAACCCCGTAATTTTGGTGAG  >  NC_000913/1433625‑1433808                                                                                              |                                                                                           gtggtCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGaaa                                                                                      >  1:1463107/1‑100 (MQ=18) gtggtCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGaaa                                                                                      >  1:1908984/1‑100 (MQ=18)  tggtCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGaaaa                                                                                     <  1:1752124/100‑1 (MQ=18)     tCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAaataa                                                                                  >  1:1313858/1‑100 (MQ=18)      cTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAaataat                                                                                 >  1:1043014/1‑100 (MQ=18)       tGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAAtt                                                                                >  2:1553660/1‑100 (MQ=18)        gATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTa                                                                               <  1:1247838/100‑1 (MQ=18)          tCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATg                                                                             >  1:343406/1‑100 (MQ=18)             aGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGatt                                                                          >  2:783046/1‑100 (MQ=18)              gCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGatta                                                                         >  1:494884/1‑100 (MQ=18)              gCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGatta                                                                         >  1:2079073/1‑100 (MQ=18)               cGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGattat                                                                        >  2:1964835/1‑100 (MQ=18)                 ttGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTAGTGTTCATATCATAATGCATACCAGAAAATAATTATGATTAttt                                                                      >  2:2085749/1‑100 (MQ=255)                   gATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTAttttt                                                                    >  1:1716324/1‑100 (MQ=17)                   gATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTAttttt                                                                    >  2:1620699/1‑100 (MQ=18)                   gATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTAttttt                                                                    >  2:65361/1‑100 (MQ=18)                   gATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTAttttt                                                                    >  2:272187/1‑100 (MQ=18)                    atatCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTtg                                                                   <  2:138587/100‑1 (MQ=17)                     tatCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTtgt                                                                  <  1:574211/100‑1 (MQ=17)                      atCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTtgtg                                                                 >  2:2478027/1‑100 (MQ=18)                      atCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTtgtg                                                                 >  1:1341251/1‑100 (MQ=18)                      atCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTtgtg                                                                 <  2:1502593/100‑1 (MQ=17)                       tCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGc                                                                >  1:1486150/1‑100 (MQ=18)                       tCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGc                                                                >  2:182099/1‑100 (MQ=17)                       tCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGc                                                                >  1:538528/1‑100 (MQ=18)                         cGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCat                                                              >  1:1483421/1‑100 (MQ=17)                          gACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCata                                                             <  1:2264979/100‑1 (MQ=18)                           aCAATAAGCAAAAATTCTAGACATAGTGAAACTCTATACGAAATTTTTGTTCATATCATAATGCATCCCAGAAAATAATCATAATTAttttctggg                                                                <  2:1811846/96‑6 (MQ=11)                              gTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTtgttcttttt                                                           >  2:1549109/1‑91 (MQ=11)                              gTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTtg                                                         >  1:2130186/1‑100 (MQ=18)                              gTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTtg                                                         <  1:2280169/100‑1 (MQ=18)                                aaGAAAATATTCGAGACTTTTTGTGACTCTCTACGAAATTGGTGTTTATATCAGATTTCTTCTGTGAAAAGATTTATGATTATTTTTGTGCATATTtgta                                                       <  2:771891/100‑1 (MQ=2)                                   aaaaaaTTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTtgtatg                                                     <  2:919565/98‑1 (MQ=17)                                    aaaaaTTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTtgtatgta                                                   <  1:2160502/100‑1 (MQ=18)                                    aaaaaTTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTtgtatgta                                                   <  2:2221222/100‑1 (MQ=17)                                    aaaaaTTCCAGACAGATTGAGACTCTATACGAAATTGGTGTTCATATCATACTGCATCCCAGAAAATAATTATGATTATTCTTGTGCATATTtgtatgta                                                   <  2:250705/100‑1 (MQ=11)                                     aaaaTTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTac                                                  <  1:2000223/100‑1 (MQ=18)                                      aaaTTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTaca                                                 <  1:934595/100‑1 (MQ=18)                                       aaTTCGAGACATAATGAGACTCTATACGAAATTGGTGTACATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTacac                                                >  2:1582578/1‑100 (MQ=255)                                          tCGAAACATAGTGAGACTCTAAACGCAATTGCTCTACATATCATAATGCATCCCATAAAATAATTATGATTATTTTTGTGCATATTTGTATGAACACGtt                                             >  2:13635/1‑100 (MQ=11)                                           cGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTc                                            >  2:2560867/1‑100 (MQ=11)                                           cGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTc                                            >  2:1628334/1‑100 (MQ=11)                                           cGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCCCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTc                                            >  1:107877/1‑100 (MQ=11)                                                                                       atacATCCCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGAAAATAAACGAATGCGTATGCAACCCCGTAATTTTGGTgag  <  2:220504/95‑1 (MQ=0)                                                                                              |                                                                                           GTGGTCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGAAAATAAACGAATGCGTATGCAACCCCGTAATTTTGGTGAG  >  NC_000913/1433625‑1433808

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: ‑