Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,535,463	T→C	pseudogene (449/1017 nt)	yjhR →	KpLE2 phage‑like element; PLD‑like domain‑containing protein YjhR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,535,463	0	T	C	100.0%	119.3 / NA	33	pseudogene (449/1017 nt)	yjhR	KpLE2 phage‑like element; PLD‑like domain‑containing protein YjhR
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (11/22);  total (11/22)

ACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCC  >  NC_000913/4535386‑4535539                                                                              |                                                                             aCGCGCTAAAGATAGTTTTCTGGTATTTGGCGTTATGGACCTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTCAt                                                                            <  2:917616/80‑1 (MQ=255) aCGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTCAt                                                                            <  1:917617/80‑1 (MQ=255) aCGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTCAt                                                                            <  1:917615/80‑1 (MQ=255)   gcgcTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTCATTgg                                                                         <  1:917618/81‑1 (MQ=255)         aaGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTCATTGGCAAAat                                                                   <  2:917620/81‑1 (MQ=255)         aaGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTCATTGGCAAAat                                                                   <  2:917619/81‑1 (MQ=255)           gATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTCATTGGCAAAatat                                                                 <  1:917621/81‑1 (MQ=255)             tAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTCATTGGCAAAATAtct                                                               <  1:917622/81‑1 (MQ=255)               gTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTCATTGGCAAAATATctct                                                             >  1:917654/1‑81 (MQ=255)                   tCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTCATTGGCAAAATATCTCtttt                                                          <  2:917623/80‑1 (MQ=255)                       gTATTTGGCGATATGGACCTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTCATTGGCAAAATATCTCTTttcttc                                                      <  2:917624/80‑1 (MQ=255)                       gTATTTGGCGATATGGACCTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTCATTGGCAAAATATCTCTTttctt                                                       <  2:917625/79‑1 (MQ=255)                         aTTTGGCGATATGGACCTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTCATTGGCAAAATATCTCTTttctt                                                       >  2:917669/1‑77 (MQ=255)                                 atatGGACCTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTCATTGGCAAAATATCTCTTTTCTTCAGATAATAATg                                           >  1:917660/1‑81 (MQ=255)                                        ccTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTCATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCa                                    <  2:917626/81‑1 (MQ=255)                                          ttATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTCATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAAt                                  >  2:917655/1‑81 (MQ=255)                                            aTCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTCATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAAttt                                >  1:917659/1‑81 (MQ=255)                                            aTCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTCATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAAttt                                >  1:917656/1‑81 (MQ=255)                                            aTCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTCATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAAt                                  <  1:917627/79‑1 (MQ=255)                                             tCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTCATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAAttt                                <  2:917628/80‑1 (MQ=255)                                                   tGCAGCCCGCATTTTTGCCGCGAGGGTCATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTc                         <  2:917629/81‑1 (MQ=255)                                                   tGCAGCCCGCATTTTCGCCGCGAGGGTCATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTc                         <  2:917630/81‑1 (MQ=255)                                                      aGCCCGCATTTTCGCCGCGAGGGTCATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAg                       >  1:917671/1‑80 (MQ=255)                                                      aGCCCGCATTTTCGCCGCGAGGGTCATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGa                      <  2:917631/81‑1 (MQ=255)                                                       gCCCGCATTTTCGCCGCGAGGGTCATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGaa                     <  1:917632/81‑1 (MQ=255)                                                         ccGCATTTTCGCCGCGAGGGTCATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAAc                   <  1:917633/81‑1 (MQ=255)                                                           gCATTTTCGCCGCGAGGGTCATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGa                 >  2:917661/1‑81 (MQ=255)                                                              ttttCGCCGCGAGGGTCATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAg              <  1:917634/81‑1 (MQ=255)                                                               tttCGCCGCGAGGGTCATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAg              >  1:917635/1‑80 (MQ=255)                                                                ttCGCCGCGAGGGTCATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGa            >  1:917666/1‑81 (MQ=255)                                                                  cgccgcGAGGGTCATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGAtt          >  2:917668/1‑81 (MQ=255)                                                                    ccgcGAGGGTCATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTa        <  1:917636/81‑1 (MQ=255)                                                                          gggTCATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTcc  <  1:917637/81‑1 (MQ=255)                                                                              |                                                                             ACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCC  >  NC_000913/4535386‑4535539

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑