Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,756,508	T→C	V117A (GTG→GCG)	intA →	CP4‑57 prophage; integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,756,508	0	T	C	100.0%	164.0 / NA	46	V117A (GTG→GCG)	intA	CP4‑57 prophage; integrase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (18/28);  total (18/28)

AACTCAGAGCCGAATCTAAAGTTTTATTGGCGAAAGACATTGATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCGGTGATATCAGTATCACTGAGATTAAGGCTCATACTCTGGTTAAAGCAGT  >  NC_000913/2756376‑2756634                                                                                                                                     |                                                                                                                               aaCTCAGAGCCGAATCTAAAGTTTTATTGGCGAAAGACATTGATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGaaa                                                                                                                         <  2:300184/140‑1 (MQ=255) aaCTCAGAGCCGAATCTAAAGTTTTATTGGCGAAAGACATTGATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGaaa                                                                                                                         <  2:293636/140‑1 (MQ=255) aaCTCAGAGCCGAATCTAAAGTTTTATTGGCGAAAGACATTGATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGaaa                                                                                                                         <  1:464507/140‑1 (MQ=255)      agagCCGAATCTAAAGTTTTATTGGCGAAAGACATTGATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAg                                                                                                                    <  2:684429/140‑1 (MQ=255)      agagCCGAATCTAAAGTTTTATTGGCGAAAGACATTGATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAg                                                                                                                    <  2:311575/140‑1 (MQ=255)       gagCCGAATCTAAAGTTTTATTGGCGAAAGACATTGATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGaaa                                                                                                                         >  2:980794/1‑134 (MQ=255)       gagCCGAATCTAAAGTTTTATTGGCGAAAGACATTGATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGaaa                                                                                                                         <  1:980794/134‑1 (MQ=255)        agCCGAATCTAAAGTTTTATTGGCGAAAGACATTGATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATCCCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCg                                                                                                                  <  1:850466/140‑1 (MQ=255)             aaTCTAAAGTTTTATTGGCGAAAGACATTGATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACa                                                                                                             >  2:398285/1‑140 (MQ=255)             aaTCTAAAGTTTTATTGGCGAAAGACATTGATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACa                                                                                                             >  1:290684/1‑140 (MQ=255)                      ttttATTGGCGAAAGACATTGATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTAt                                                                                                    <  2:48727/140‑1 (MQ=255)                        ttATTGGCGAAAGACATTGATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGc                                                                                                  >  2:116036/1‑140 (MQ=255)                          aTTGGCGAAAGACATTGATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCcg                                                                                                <  2:290684/140‑1 (MQ=255)                           ttGGCGAAAGACATTGATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCcga                                                                                               <  1:441833/140‑1 (MQ=255)                                  aaGACATTGATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATc                                                                                        <  2:540346/140‑1 (MQ=255)                                        ttGATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGgcgc                                                                                  >  2:52344/1‑140 (MQ=255)                                          gATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGcgctc                                                                                <  1:700811/140‑1 (MQ=255)                                              cTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCtt                                                                            >  2:950943/1‑140 (MQ=255)                                                      cATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTgagagaga                                                                    >  2:260466/1‑140 (MQ=255)                                                             aagaaCAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTc                                                             >  2:725511/1‑140 (MQ=255)                                                               gaaCAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCtt                                                                            <  2:968771/123‑1 (MQ=255)                                                               gaaCAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCtt                                                                            >  1:968771/1‑123 (MQ=255)                                                                 aCAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCgg                                                         >  2:360737/1‑140 (MQ=255)                                                                    ggTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCaa                                                      <  1:453418/140‑1 (MQ=255)                                                                        aGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCgg                                                  >  1:1015199/1‑140 (MQ=255)                                                                         ggAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCGGt                                                 <  1:780097/140‑1 (MQ=255)                                                                          gAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCGGTg                                                >  1:271774/1‑140 (MQ=255)                                                                            aTTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCGGTGat                                              <  2:180492/140‑1 (MQ=255)                                                                            aTTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCGGTGat                                              <  1:360737/140‑1 (MQ=255)                                                                            aTTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCGGTGat                                              <  1:52344/140‑1 (MQ=255)                                                                              tctcAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCGGTGatat                                            <  1:90370/140‑1 (MQ=255)                                                                                   agagGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCGGTGATATCAGTa                                       <  1:83094/140‑1 (MQ=255)                                                                                    gagGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCGGTGATATCAGTAt                                      <  1:245841/140‑1 (MQ=255)                                                                                        ccAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCGGTGATATCAGTATCACt                                  <  1:950943/140‑1 (MQ=255)                                                                                                aaTACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCGGTGATATCAGTATCACTGAGATTaa                          <  2:46873/140‑1 (MQ=255)                                                                                                       tcttGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCGGTGATATCAGTATCACTGAGATTAAGGCTCAt                   >  2:949213/1‑140 (MQ=255)                                                                                                         ttGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCGGTGATATCAGTATCACTGAGAtt                            <  1:958762/129‑1 (MQ=255)                                                                                                         ttGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCGGTGATATCAGTATCACTGAGAtt                            >  2:958762/1‑129 (MQ=255)                                                                                                          tGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCGGTGATATCAGTATCACTGAGATTAAGGCTCATAct                <  2:1015199/140‑1 (MQ=255)                                                                                                          tGTTAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCGGTGATATCAGTATCACTGAGATTAAGGCTCATAct                <  2:831500/140‑1 (MQ=255)                                                                                                            ttAGTTGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCGGTGATATCAGTATCACTGAGATTAAGGCTCATActct              >  2:770851/1‑140 (MQ=255)                                                                                                                ttGCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCGGTGATATCAGTATCACTGAGATTAAGGCTCATACTCTGGtt          >  1:617688/1‑140 (MQ=255)                                                                                                                  gCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCGGTGATATCAGTATCACTGAGATTaa                          <  1:113178/122‑1 (MQ=255)                                                                                                                  gCCGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCGGTGATATCAGTATCACTGAGATTaa                          >  2:113178/1‑122 (MQ=255)                                                                                                                   ccGAGCGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCACTCGCTTGAGAGAGATATTTTCCCGGCAATCGGTGATATCAGTATCACTGAGATTAAGGCTCATACTCTGGTTaaa       <  1:1034985/140‑1 (MQ=255)                                                                                                                        cGTTGGTGGAATGCGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCGGTGATATCAGTATCACTGAGATTAAGGCTCATACTCTGGTTAAAGCAGt  >  2:269915/1‑140 (MQ=255)                                                                                                                                     |                                                                                                                               AACTCAGAGCCGAATCTAAAGTTTTATTGGCGAAAGACATTGATCCTCAGGAACATCAGAAAGAACAGGTGAGGAATTCTCAAGAGGCCAAAACCAATACCTTCTTGTTAGTTGCCGAGCGTTGGTGGAATGTGAAGAAAACCAGCGTAACAGAGGACTATGCCGACGATATCTGGCGCTCGCTTGAGAGAGATATTTTCCCGGCAATCGGTGATATCAGTATCACTGAGATTAAGGCTCATACTCTGGTTAAAGCAGT  >  NC_000913/2756376‑2756634

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: ‑