Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,647,076	T→C	intergenic (+339/+98)	flxA → / ← ydfW	Qin prophage; protein FlxA/Qin prophage; uncharacterized protein YdfW

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,647,076	0	T	C	100.0%	129.1 / NA	37	intergenic (+339/+98)	flxA/ydfW	Qin prophage; protein FlxA/Qin prophage; uncharacterized protein YdfW
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (21/16);  total (21/16)

ACTTTTGTGGGGACAGTCCACAAAACTGCCAACTTCCGCTTCTTGCTCTTAGCGGACATTAGCATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGTAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCGAATCGATCTTGGTTTCAATCTTTTTTATCGGGATCAGGCTTCTTTTTAGGT  >  NC_000913/1646939‑1647210                                                                                                                                          |                                                                                                                                       aCTTTTGTGGGGACAGTCCACAAAACTGCCAACTTCCGCTTCTTGCTCTTAGCGGACATTAGCATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCaa                                                                                                                                      >  2:464390/1‑140 (MQ=255)   ttttGTGGGGACAGTCCACAAAACTGCCAACTTCCGCTTCTTGCTCTTAGCGGACATTAGCATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCaaaa                                                                                                                                    >  1:561074/1‑140 (MQ=255)    tttGTGGGGACAGTCCACAAAACTGCCAACTTCCGCTTCTTGCTCTTAGCGGACATTAGCATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAAc                                                                                                                                   <  2:391612/140‑1 (MQ=255)     ttGTGGGGACAGTCCACAAAACTGCCAACTTCCGCTTCTTGCTCTTAGCGGACATTAGCATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAACa                                                                                                                                  <  2:260317/140‑1 (MQ=255)                 tCCACAAAACTGCCAACTTCCGCTTCTTGCTCTTAGCGGACATTAGCATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACaaa                                                                                                                         >  1:272484/1‑137 (MQ=255)                 tCCACAAAACTGCCAACTTCCGCTTCTTGCTCTTAGCGGACATTAGCATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACaaa                                                                                                                         <  2:272484/137‑1 (MQ=255)                      aaaaCTGCCAACTTCCGCTTCTTGCTCTTAGCGGACATTAGCATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGa                                                                                                                 <  1:577892/140‑1 (MQ=255)                             ccAACTTCCGCTTCTTGCTCTTAGCGGACATTAGCATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGaa                                                                                                          >  1:145864/1‑140 (MQ=255)                                        ttcttGCTCTTAGCGGACATTAGCATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAAcg                                                                                               <  2:561074/140‑1 (MQ=255)                                          cttGCTCTTAGCGGACATTAGCATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGaa                                                                                                          <  2:492695/127‑1 (MQ=255)                                          cttGCTCTTAGCGGACATTAGCATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGaa                                                                                                          >  1:492695/1‑127 (MQ=255)                                                  tAGCGGACATTAGCATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGa                                                                                     >  1:28346/1‑140 (MQ=255)                                                       gACATTAGCATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTa                                                                                >  1:376007/1‑140 (MQ=255)                                                         cATTAGCATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTAcc                                                                              <  1:601712/140‑1 (MQ=255)                                                         cATTAGCATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTAcc                                                                              <  1:48019/140‑1 (MQ=255)                                                           ttAGCATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCt                                                                            <  1:535338/140‑1 (MQ=255)                                                               cATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGa                                                                        >  2:397710/1‑140 (MQ=255)                                                                    gCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGaa                                                                       <  2:364283/136‑1 (MQ=255)                                                                    gCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGaa                                                                       >  1:364283/1‑136 (MQ=255)                                                                    gCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGa                                                                   >  2:329049/1‑140 (MQ=255)                                                                    gCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGa                                                                   >  2:527486/1‑140 (MQ=255)                                                                     cTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGat                                                                  <  1:464390/140‑1 (MQ=255)                                                                        tttACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATg                                                               >  1:204655/1‑140 (MQ=255)                                                                              aTAACGCCTCATTACGCGCACCGCCCAGACTGACTCAACGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACTCa                                                         >  1:122404/1‑140 (MQ=255)                                                                                  cGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCg                                                     >  1:1700/1‑140 (MQ=255)                                                                                  cGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCg                                                     >  1:308047/1‑140 (MQ=255)                                                                                          tACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCGAAt                                                  <  1:660530/135‑1 (MQ=255)                                                                                          tACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCGAAt                                                  >  2:660530/1‑135 (MQ=255)                                                                                              cgcACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACt                                                           >  2:610507/1‑122 (MQ=255)                                                                                              cgcACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACt                                                           <  1:610507/122‑1 (MQ=255)                                                                                                             gactCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCGAATCGATCTTGGTTTCAATCTTTTTTa                          >  1:314579/1‑140 (MQ=255)                                                                                                             gactCAGCGCGTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCGAATCGATCTTGGTTTCAATCTTTTTTa                          >  1:295922/1‑140 (MQ=255)                                                                                                                    cgcgTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCGAATCGATCTTGGTTTCAATCTTTTTTATCGGGAt                   <  2:1700/140‑1 (MQ=255)                                                                                                                    cgcgTTTCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCGAATCGATCTTGGTTTCAATCTTTTTTATCGGGAt                   >  1:83312/1‑140 (MQ=255)                                                                                                                         ttCTGGCATATCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCGAATCGATCTTGGTTTCAATCTTTTTTATCGGGATCAGGc              <  1:364915/140‑1 (MQ=255)                                                                                                                                   tCCCCGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCGAATCGATCTTGGTTTCAATCTTTTTTATCGGGATCAGGCTTCTTTTTAg    >  2:154814/1‑140 (MQ=255)                                                                                                                                     cccGGCAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCGAATCGATCTTGGTTTCAATCTTTTTTATCGGGATCAGGCTTCTTTTTAGGt  <  2:83312/140‑1 (MQ=255)                                                                                                                                          |                                                                                                                                       ACTTTTGTGGGGACAGTCCACAAAACTGCCAACTTCCGCTTCTTGCTCTTAGCGGACATTAGCATAGGCTATTTACCATAACGCCTCATTACGCGCACCGCCCAGACTGACTCAGCGCGTTTCTGGCATATCCCCGGTAAAACAAGTAACAAACCACCCGAAAATGAACACCAGAAACGCGACTTAAGAATCTACCCTATGAATGGATATGCACTCAACCGAATCGATCTTGGTTTCAATCTTTTTTATCGGGATCAGGCTTCTTTTTAGGT  >  NC_000913/1646939‑1647210

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: ‑