Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,535,441	C→T	pseudogene (439/1029 nt)	yjhR →	pseudogene, helicase family, putative frameshift suppressor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,535,441	0	C	T	100.0%	115.9 / NA	36	pseudogene (439/1029 nt)	yjhR	pseudogene, helicase family, putative frameshift suppressor
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (19/17);  total (19/17)

TCAAAACATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCATGGTGTGGAG  >  NC_000913/4535324‑4535575                                                                                                                      |                                                                                                                                       tCAAAACATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCTTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGt                                                                                                                   >  2:121650/1‑139 (MQ=255)     aaCATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTAtt                                                                                                               >  1:107284/1‑139 (MQ=255)      aCATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTg                                                                                                              >  2:324177/1‑139 (MQ=255)      aCATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTg                                                                                                              >  2:149653/1‑139 (MQ=255)          gAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCaa                                                                                                          >  1:54616/1‑139 (MQ=255)          gAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTCATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCaa                                                                                                          >  1:310166/1‑139 (MQ=255)           aaGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCaaa                                                                                                         <  1:148964/139‑1 (MQ=255)               tGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAatat                                                                                                     <  2:54616/139‑1 (MQ=255)                      tttCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCtttt                                                                                              <  1:377122/139‑1 (MQ=255)                      tttCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCtttt                                                                                              <  2:310166/139‑1 (MQ=255)                           tGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCa                                                                                         <  1:130122/139‑1 (MQ=255)                           tGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCa                                                                                         <  2:44276/139‑1 (MQ=255)                                            tCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCa                                                                        >  2:764217/1‑139 (MQ=255)                                                        cTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCa                                                            >  1:644163/1‑139 (MQ=255)                                                        cTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCa                                                            >  2:566765/1‑139 (MQ=255)                                                        cTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCa                                                            >  1:55698/1‑139 (MQ=255)                                                               aCGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCa                                                                                         <  1:611758/103‑1 (MQ=255)                                                               aCGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCa                                                                                         >  2:611758/1‑103 (MQ=255)                                                                cgcgCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGa                                                                                                                       <  2:208445/72‑1 (MQ=255)                                                                cgcgCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGa                                                                                                                       >  1:208445/1‑72 (MQ=255)                                                                     tAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGAt                                               >  2:177080/1‑139 (MQ=255)                                                                             gTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTc                                       >  2:65470/1‑139 (MQ=255)                                                                               tttCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCg                                     <  2:55698/139‑1 (MQ=255)                                                                                        tttGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATacac                            >  1:534719/1‑139 (MQ=255)                                                                                          tGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCg                                     >  1:55713/1‑128 (MQ=255)                                                                                          tGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCg                                     <  2:55713/128‑1 (MQ=255)                                                                                                tatGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCa                    >  2:358970/1‑139 (MQ=255)                                                                                                  tGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAAc                  >  1:69821/1‑139 (MQ=255)                                                                                                        ttATCGAGATTCAGTCCGCATATTCGCCGCGAGAGTTACTAGCAAAATATCTCGTTTCTTCAGATAATAATGCGCTGCAATTTGAGTTCCAGAAACGACAGGACTTAAGTTCCGCACATACACAAATTTGAACGCTGCa            <  2:637176/139‑1 (MQ=255)                                                                                                        ttATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCa            <  1:324177/139‑1 (MQ=255)                                                                                                        ttATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCa            <  2:644163/139‑1 (MQ=255)                                                                                                        ttATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCa            <  1:764217/139‑1 (MQ=255)                                                                                                        ttATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCa            <  2:69821/139‑1 (MQ=255)                                                                                                        ttATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCa            <  2:107284/139‑1 (MQ=255)                                                                                                            cGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCATGgt        <  2:534719/139‑1 (MQ=255)                                                                                                              agaTGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCATGgtgt      >  2:539300/1‑139 (MQ=255)                                                                                                                  gCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCATGGTGTGGag  <  1:539300/139‑1 (MQ=255)                                                                                                                      |                                                                                                                                       TCAAAACATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCATGGTGTGGAG  >  NC_000913/4535324‑4535575

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: ‑