Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,471,767	(C)5→6	pseudogene (356/579 nt)	yfdL ←	pseudogene, CPS‑53 (KpLE1) prophage,Phage or Prophage Related

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,471,762	1	.	C	100.0%	103.5 / NA	31	pseudogene (361/579 nt)	yfdL	pseudogene, CPS‑53 (KpLE1) prophage,Phage or Prophage Related
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (17/14);  total (17/14)

CCGGCACAAGCTATATAGCCAACATTTGCACTGCCGGGAGTGTAATCCTGAGTCGCAAATACCCGCAGACATCTATTCGGAAATGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGG‑CCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGAAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTCCCTACATTTCTTTTAGCCGC  >  NC_000913/2471626‑2471882                                                                                                                                          |                                                                                                                         ccGGCACAAGCTATATAGTCAACATTTGCACTGCCGGGAGTGTAATCCTGAGTCGCAAATACCCGCAGACATCTATTCGGAAATGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGG‑cc                                                                                                                        <  1:722025/139‑1 (MQ=255)                   ccAACATTTGCACTGCCGGGAGTGTAATCCTGAGTCGCAAATACCCGCAGACATCTATTCGGAAATGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCCATTGAATAATTaaa                                                                                                       >  2:138904/1‑139 (MQ=255)                    cAACATTTGTACTGCCGGGAGTGTAATCCTGAGTCGCAAATACCCGCAGACATCTATTCGGAAATGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCCATTGAATAATTAAAc                                                                                                      >  1:743190/1‑139 (MQ=255)                     aaCATTTGCACTGCCGGGAGTGTAATCCTGAGTCGCAAATACCCGCAGACATCTATTCGGAAATGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCCATTGAATAATTAAAcc                                                                                                     >  1:1022127/1‑139 (MQ=255)                        aTTTGCACTGCCGGGAGTGTAATCCTGAGTCGCAAATACCCGCAGACATCTATTCGGAAATGCAATCTGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCCATTGa                                                                                                                >  2:627689/1‑125 (MQ=255)                        aTTTGCACTGCCGGGAGTGTAATCCTGAGTCGCAAATACCCGCAGACATCTATTCGGAAATGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCCATTGa                                                                                                                <  1:627689/125‑1 (MQ=255)                           tGCACTGCCGGGAGTGTAATCCTGAGTCGCAAATACCCGCAGACATCTATTCGGAAATGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCCATTGAATAATTAAACCGGATgg                                                                                               >  2:525727/1‑139 (MQ=255)                                  ccGGGAGTGTAATCCTGAGTCGCAAATACCCGCAGACATCTATTCGGAAATGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCCATTGAATAATTAAACCGGATGGCAAtttt                                                                                        >  1:23538/1‑139 (MQ=255)                                         tgtAATCCTGAGTCGCAAATACCCGCAGACATCTATTCGGAAATGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATc                                                                                 >  1:251754/1‑139 (MQ=255)                                                   aGTCGCAAATACCCGCAGACATCTATTCGGAAATGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGa                                                                       >  2:99586/1‑139 (MQ=255)                                                         aaaTACCCGCAGACATCTATTCGGAAATGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGa                                                                 <  1:901873/139‑1 (MQ=255)                                                                   aGACATCTATTCGGAAATGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGAAAGCATaaaa                                                       <  2:1022127/139‑1 (MQ=255)                                                                   aGACATCTATTCGGAAATGCAATCGGAAAATAGGTTACCGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGAAAGCATaaaa                                                       <  2:713802/139‑1 (MQ=255)                                                                       aTCTATTCGGAAATGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGAAAGCATAAAACTAc                                                   >  2:1068912/1‑139 (MQ=255)                                                                        tCTATTCGGAAATGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGAAAGCATAAAACTAcc                                                  <  2:251754/139‑1 (MQ=255)                                                                            ttCGGAAATGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGAAAGCATAAAACTACCCata                                              <  1:525727/139‑1 (MQ=255)                                                                            ttCGGAAATGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGG‑cc                                                                                                                        >  1:889408/1‑64 (MQ=255)                                                                            ttCGGAAATGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGG‑cc                                                                                                                        <  2:889408/64‑1 (MQ=255)                                                                                    tGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGG‑cc                                                                                                                        <  1:899890/56‑1 (MQ=255)                                                                                    tGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGG‑cc                                                                                                                        >  2:899890/1‑56 (MQ=255)                                                                                      cAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGAAAGCATAAAACTACCCat                                               >  1:1018643/1‑128 (MQ=255)                                                                                      cAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGAAAGCATAAAACTACCCat                                               <  2:1018643/128‑1 (MQ=255)                                                                                      cAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGAAAGCATAAAACTACCCATATCAGGTATCt                                    >  1:487709/1‑139 (MQ=255)                                                                                           ggAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGG‑cccccca                                                                                                                   >  1:634667/1‑52 (MQ=255)                                                                                           ggAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGG‑cccccca                                                                                                                   <  2:634667/54‑3 (MQ=255)                                                                                               aaTAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGAAAGCATAAAACTACCCATATCAGGTATCTGATTCGccc                           <  1:1068912/139‑1 (MQ=255)                                                                                                      tACTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGAAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTccc                    <  2:743190/139‑1 (MQ=255)                                                                                                       aCTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGAAAGCATAAAACTa                                                    <  1:29367/106‑1 (MQ=255)                                                                                                       aCTGTGTCCTGAGACGTCAGCGGAACATCAATTGGCCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGAAAGCATAAAACTa                                                    >  2:29367/1‑106 (MQ=255)                                                                                                           tgtCCTGAGACGTCAGCGGAACATCAATTGGCCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGAAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGt                       <  2:328128/131‑1 (MQ=255)                                                                                                           tgtCCTGAGACGTCAGCGGAACATCAATTGGCCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGAAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGt                       >  1:328128/1‑131 (MQ=255)                                                                                                                  agaCGTCAGCGGAACATCAATTGGCCCCCCATTGa                                                                                                                <  2:601988/35‑1 (MQ=255)                                                                                                                  agaCGTCAGCGGAACATCAATTGGCCCCCCATTGa                                                                                                                >  1:601988/1‑35 (MQ=255)                                                                                                                       tCAGCGGAACATCAATTGGCCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGAAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTCCCTACATTTCTTTTAGCCg   >  2:1043066/1‑139 (MQ=255)                                                                                                                       tCAGCGGAACATCAATTGGCCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGAAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTCCCTACATTTCTTTTAGCCg   >  2:869059/1‑139 (MQ=255)                                                                                                                        cAGCGGAACATCAATTGGCCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGAAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTCCCTACATTTCTTTTAGCCGc  <  1:1043066/139‑1 (MQ=255)                                                                                                                                cATCAATTGGCCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGAAAGCATAAAACTACCCATATCAGGTATCTGATTc                               <  2:932922/102‑1 (MQ=255)                                                                                                                                cATCAATTGGCCCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGAAAGCATAAAACTACCCATATCAGGTATCTGATTc                               >  1:932922/1‑102 (MQ=255)                                                                                                                                          |                                                                                                                         CCGGCACAAGCTATATAGCCAACATTTGCACTGCCGGGAGTGTAATCCTGAGTCGCAAATACCCGCAGACATCTATTCGGAAATGCAATCGGAAAATAGGTTACTGTGTCCTGAGACGTCAGCGGAACATCAATTGG‑CCCCCATTGAATAATTAAACCGGATGGCAATTTTTGATATCCAGGAACTGAAGCAGAAAGCATAAAACTACCCATATCAGGTATCTGATTCGCCCCTGTCCCTACATTTCTTTTAGCCGC  >  NC_000913/2471626‑2471882

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑