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%	133.9 / NA	42	pseudogene (439/1029 nt)	yjhR	pseudogene, helicase family, putative frameshift suppressor
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (20/22);  total (20/22)

TCCTGTCTACTCAAAACATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCA  >  NC_000913/4535314‑4535565                                                                                                                                |                                                                                                                             tcCTGTCTACTCAAAACATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTcg                                                                                                                   >  1:1044626/1‑139 (MQ=255) tcCTGTCTACTCAAAACATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTcg                                                                                                                   >  1:895661/1‑139 (MQ=255)                aCATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTg                                                                                                    >  1:674984/1‑139 (MQ=255)                 cATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTgg                                                                                                   <  1:409968/139‑1 (MQ=255)                    gAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCa                                                                                                 <  2:632667/138‑1 (MQ=255)                    gAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCa                                                                                                 >  1:632667/1‑138 (MQ=255)                                  tCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTttct                                                                                  <  2:895661/139‑1 (MQ=255)                                     tGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCa                                                                               <  2:674984/139‑1 (MQ=255)                                                      tCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCa                                                                               >  2:416592/1‑122 (MQ=255)                                                      tCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCa                                                                               <  1:416592/122‑1 (MQ=255)                                                                tGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTttctt                                                                                 >  2:452641/1‑110 (MQ=255)                                                                tGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTttctt                                                                                 <  1:452641/110‑1 (MQ=255)                                                                tGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGataata                                                                        >  1:464502/1‑119 (MQ=255)                                                                tGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGataata                                                                        <  2:464502/119‑1 (MQ=255)                                                                tGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCa                                                              >  2:1161552/1‑129 (MQ=255)                                                                tGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCa                                                              <  1:1161552/129‑1 (MQ=255)                                                                 gCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTc                                                   >  1:64296/1‑139 (MQ=255)                                                                         aCGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGa                                           <  2:378183/139‑1 (MQ=255)                                                                                       gTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTc                             >  1:1079494/1‑139 (MQ=255)                                                                                         tttCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCa                                                                                                 >  1:331663/1‑69 (MQ=255)                                                                                         tttCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCa                                                                                                 <  2:331663/69‑1 (MQ=255)                                                                                           tCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGca                         >  1:952116/1‑139 (MQ=255)                                                                                             tGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCAtttt                                                                                                                     >  1:394971/1‑45 (MQ=255)                                                                                             tGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCAtttt                                                                                                                     <  2:394971/45‑1 (MQ=255)                                                                                                  tttGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATacac                  >  2:584004/1‑139 (MQ=255)                                                                                                             ggACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCa                                                                               >  2:230691/1‑67 (MQ=255)                                                                                                             ggACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCa                                                                               <  1:230691/67‑1 (MQ=255)                                                                                                             ggACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACg       <  2:1079494/139‑1 (MQ=255)                                                                                                             ggACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACg       <  2:64296/139‑1 (MQ=255)                                                                                                                  ttATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCTAAATATCTCTTTTCTTCAGATAATAATGCGTAGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCa  <  1:890233/139‑1 (MQ=255)                                                                                                                  ttATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCa  <  1:1159263/139‑1 (MQ=255)                                                                                                                  ttATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCa  <  2:952116/139‑1 (MQ=255)                                                                                                                   tATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCa  >  1:433222/1‑138 (MQ=255)                                                                                                                   tATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCa  <  2:433222/138‑1 (MQ=255)                                                                                                                    aTCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTttcttc                                                                                >  1:637113/1‑59 (MQ=255)                                                                                                                    aTCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTttcttc                                                                                <  2:637113/59‑1 (MQ=255)                                                                                                                    aTCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTttct                                                                                  <  2:201909/57‑1 (MQ=255)                                                                                                                    aTCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTttct                                                                                  >  1:201909/1‑57 (MQ=255)                                                                                                                    aTCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATaataat                                                                      <  1:360191/69‑1 (MQ=255)                                                                                                                    aTCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATaataat                                                                      >  2:360191/1‑69 (MQ=255)                                                                                                                          aTGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCTAAATATCTCGTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGaaa                                              <  1:843975/87‑1 (MQ=255)                                                                                                                          aTGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAATTTCAGaaa                                              >  2:843975/1‑87 (MQ=255)                                                                                                                                |                                                                                                                             TCCTGTCTACTCAAAACATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCA  >  NC_000913/4535314‑4535565

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑