Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,765,829	(C)5→4	intergenic (‑53/‑89)	yfjM ← / → rnlA	CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, RNase LS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,765,825	0	C	.	100.0%	273.3 / NA	64	intergenic (‑49/‑93)	yfjM/rnlA	CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, RNase LS
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (34/30);  total (34/30)

TGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTCAGGGCA  >  NC_000913/2765696‑2765959                                                                                                                                  |                                                                                                                                       tgGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCa                                                                                                                              <  1:559842/139‑1 (MQ=255)                   tATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCaa                                                                                                            >  1:942118/1‑139 (MQ=255)                             ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                                     >  1:1050011/1‑136 (MQ=255)                             ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                                     <  2:1050011/136‑1 (MQ=255)                              tgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACt                                                                                                 <  1:1119653/139‑1 (MQ=255)                                     tGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                                                               <  1:853096/118‑1 (MQ=255)                                     tGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                                                               >  2:853096/1‑118 (MQ=255)                                       agaTCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAgggggg                                                                                        <  1:655522/139‑1 (MQ=255)                                                   ggTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCaa                                                                                                       <  1:200011/112‑1 (MQ=255)                                                   ggTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCaa                                                                                                       >  2:200011/1‑112 (MQ=255)                                                    gTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTagag                                                                           >  2:138929/1‑139 (MQ=255)                                                      tACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAgggggg                                                                                        <  2:1274953/124‑1 (MQ=255)                                                      tACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAgggggg                                                                                        >  1:1274953/1‑124 (MQ=255)                                                      tACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAg                                                                                             <  1:342602/119‑1 (MQ=255)                                                      tACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAg                                                                                             >  2:342602/1‑119 (MQ=255)                                                        ccGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTc                                                                       >  2:451393/1‑139 (MQ=255)                                                         cGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTcc                                                                      <  1:451393/139‑1 (MQ=255)                                                             aCGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAgg                                                                                            <  2:536290/113‑1 (MQ=255)                                                             aCGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAgg                                                                                            >  1:536290/1‑113 (MQ=255)                                                              cGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAggg                                                                                           <  2:181946/113‑1 (MQ=255)                                                              cGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAggg                                                                                           >  1:181946/1‑113 (MQ=255)                                                                          tcCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATggg                                                     >  1:125954/1‑139 (MQ=255)                                                                           cccccATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTcccc                                                                    >  2:211249/1‑123 (MQ=255)                                                                           cccccATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTcccc                                                                    <  1:211249/123‑1 (MQ=255)                                                                           cccccATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGa                                                    >  1:1245707/1‑139 (MQ=255)                                                                             cccATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGc                                                                                                                                        <  1:508348/54‑1 (MQ=255)                                                                             cccATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGc                                                                                                                                        >  2:508348/1‑54 (MQ=255)                                                                                  tttGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGTCTAAATTTAGCAAATCAATACACTTCAGGGGGGta                                                                                      >  2:410875/1‑98 (MQ=255)                                                                                  tttGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGta                                                                                      <  1:410875/98‑1 (MQ=255)                                                                                      tgGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGc                                                                                                                                        <  2:454199/45‑1 (MQ=255)                                                                                      tgGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGc                                                                                                                                        >  1:454199/1‑45 (MQ=255)                                                                                           tGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                                                               >  2:269144/1‑64 (MQ=255)                                                                                           tGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                                                               <  1:269144/64‑1 (MQ=255)                                                                                           tGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAAt                                    >  2:292386/1‑139 (MQ=255)                                                                                            gCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATc                                   >  2:450954/1‑139 (MQ=255)                                                                                             cccccccGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CGCCTATTCAGGTGGCTAAATTTAGCAAAt                                                                                                          <  1:803651/67‑1 (MQ=255)                                                                                             cccccccGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                                                               <  2:496359/62‑1 (MQ=255)                                                                                             cccccccGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                                                               >  1:496359/1‑62 (MQ=255)                                                                                             cccccccGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAAt                                                                                                          >  2:803651/1‑67 (MQ=255)                                                                                             cccccccGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGta                                                                                      <  2:498444/87‑1 (MQ=255)                                                                                             cccccccGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGta                                                                                      >  1:498444/1‑87 (MQ=255)                                                                                                            aTCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGGGt                                                                          <  1:227958/84‑1 (MQ=255)                                                                                                            aTCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGGGt                                                                          >  2:227958/1‑84 (MQ=255)                                                                                                            aTCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACt                   <  2:942118/139‑1 (MQ=255)                                                                                                              ccTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTa                 >  2:8544/1‑139 (MQ=255)                                                                                                                tGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAgggggg                                                                                        <  2:506335/66‑1 (MQ=255)                                                                                                                tGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAgggggg                                                                                        >  1:506335/1‑66 (MQ=255)                                                                                                                 gCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTGTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAAt              >  2:783297/1‑139 (MQ=255)                                                                                                                  cccTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAggg                                                                                           <  2:76928/61‑1 (MQ=255)                                                                                                                  cccTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAggg                                                                                           >  1:76928/1‑61 (MQ=255)                                                                                                                     tataGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCata                                                                 >  2:900074/1‑84 (MQ=255)                                                                                                                     tataGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCata                                                                 <  1:900074/84‑1 (MQ=255)                                                                                                                       taGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAAt                                                                                                          <  2:621958/41‑1 (MQ=255)                                                                                                                       taGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAAt                                                                                                          >  1:621958/1‑41 (MQ=255)                                                                                                                       taGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGta                                                                                      >  1:233796/1‑61 (MQ=255)                                                                                                                       taGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGta                                                                                      <  2:233796/61‑1 (MQ=255)                                                                                                                       taGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCatat                                                                >  1:263456/1‑83 (MQ=255)                                                                                                                       taGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCatat                                                                <  2:263456/83‑1 (MQ=255)                                                                                                                       taGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTa                                                         >  1:551856/1‑90 (MQ=255)                                                                                                                       taGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTa                                                         <  2:551856/90‑1 (MQ=255)                                                                                                                       taGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGaa                                            >  1:408753/1‑103 (MQ=255)                                                                                                                       taGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGaa                                            <  2:408753/103‑1 (MQ=255)                                                                                                                       taGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTc        <  2:125954/139‑1 (MQ=255)                                                                                                                            ggAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                                     <  2:302781/41‑1 (MQ=255)                                                                                                                            ggAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                                     >  1:302781/1‑41 (MQ=255)                                                                                                                            ggAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTCAGGGc   >  1:608298/1‑139 (MQ=255)                                                                                                                            ggAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTCAGGGc   >  1:390123/1‑139 (MQ=255)                                                                                                                             gAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTCAGGGCa  <  1:644416/139‑1 (MQ=255)                                                                                                                                  |                                                                                                                                       TGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTCAGGGCA  >  NC_000913/2765696‑2765959

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑