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%	157.3 / NA	38	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 . (17/21);  total (17/21)

AGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTC  >  NC_000913/2765712‑2765953                                                                                                                    |                                                                                                                                 aGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                                                         <  1:228948/139‑1 (MQ=255) aGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                                                         <  2:825746/139‑1 (MQ=255) aGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                                                         <  2:178972/139‑1 (MQ=255) aGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                                                         <  2:646074/139‑1 (MQ=255) aGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                                                         >  2:851589/1‑139 (MQ=255) aGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                                                         >  1:825746/1‑139 (MQ=255) aGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                                                         <  1:851589/139‑1 (MQ=255)      cGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAAt                                                                                                    <  2:423748/139‑1 (MQ=255)      cGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCTCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAAt                                                                                                    >  1:539603/1‑139 (MQ=255)             ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATaca                                                                                             >  2:676945/1‑139 (MQ=255)             ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATaca                                                                                             >  2:410264/1‑139 (MQ=255)                     tGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAggg                                                                                     <  1:319082/139‑1 (MQ=255)                     tGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAggg                                                                                     <  1:676945/139‑1 (MQ=255)                        gaTCAGGAAGAGGTTTCCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAgggggg                                                                                  <  2:833538/139‑1 (MQ=255)                            aGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                               >  1:543260/1‑122 (MQ=255)                            aGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                               <  2:543260/122‑1 (MQ=255)                                   ggTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAggg                                                                                     >  1:493126/1‑125 (MQ=255)                                   ggTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAggg                                                                                     <  2:493126/125‑1 (MQ=255)                                   ggTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTag                                                                       >  2:135248/1‑139 (MQ=255)                                   ggTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTag                                                                       >  1:662168/1‑139 (MQ=255)                                      tACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGt                                                                    <  2:662168/139‑1 (MQ=255)                                             aCGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCa                                                             <  1:171966/139‑1 (MQ=255)                                                  ggACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                               <  1:553032/100‑1 (MQ=255)                                                  ggACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                               >  2:553032/1‑100 (MQ=255)                                                  ggACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGt                                                        <  2:539603/139‑1 (MQ=255)                                                         atcCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCATATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATg                                                 <  2:876866/139‑1 (MQ=255)                                                              ccATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATc                                            <  2:330483/139‑1 (MQ=255)                                                                     gtgGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                                                         <  1:935345/71‑1 (MQ=255)                                                                     gtgGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                                                         >  2:935345/1‑71 (MQ=255)                                                                      tgGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCCGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTCTTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAAt                                    >  2:170889/1‑139 (MQ=255)                                                                           tgccc‑cccccGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTaaa                                                                                                              >  2:187012/4‑60 (MQ=255)                                                                           tgccc‑cccccGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTaaa                                                                                                              <  1:187012/57‑1 (MQ=255)                                                                                                 cTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTaa          >  2:548572/1‑139 (MQ=255)                                                                                                         taGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATg                                                 >  1:868039/1‑92 (MQ=255)                                                                                                         taGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATg                                                 <  2:868039/92‑1 (MQ=255)                                                                                                         taGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTc  >  1:314663/1‑139 (MQ=255)                                                                                                              ggAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAg                                                                                       >  2:80754/1‑49 (MQ=255)                                                                                                              ggAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAg                                                                                       <  1:80754/49‑1 (MQ=255)                                                                                                                    |                                                                                                                                 AGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTC  >  NC_000913/2765712‑2765953

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑