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%	188.3 / NA	59	pseudogene (439/1029 nt)	yjhR	pseudogene, helicase family, putative frameshift suppressor
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (33/26);  total (33/26)

TCTACTCAAAACATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCATGGTGTGGAG  >  NC_000913/4535319‑4535575                                                                                                                           |                                                                                                                                       tCTACTCAAAACATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCAtttt                                                                                                                               >  2:763004/1‑132 (MQ=255) tCTACTCAAAACATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCAtttt                                                                                                                               <  1:763004/132‑1 (MQ=255)   tACTCAAAACATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAg                                                                                                                      >  2:15952/1‑139 (MQ=255)        aaaaCATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTa                                                                                                                 >  2:17701/1‑139 (MQ=255)            cATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTgg                                                                                                             <  1:1051640/139‑1 (MQ=255)             aTGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTGATCGAGATGCAGTCCGCATTTTcgccgc                                                                                                                         >  2:645237/1‑126 (MQ=255)             aTGAAGATGGCAGGTGTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTcgccgc                                                                                                                         <  1:645237/126‑1 (MQ=255)                      gCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTAt                                                                                                                <  2:549322/126‑1 (MQ=255)                      gCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTAt                                                                                                                >  1:549322/1‑126 (MQ=255)                        aGGTTTCTTGATAGCAATAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTGGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATctct                                                                                                 >  2:615310/1‑139 (MQ=255)                        aGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATctct                                                                                                 <  1:615310/139‑1 (MQ=255)                          gTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCttt                                                                                               >  1:118609/1‑139 (MQ=255)                                      cAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGataat                                                                                   >  1:284253/1‑139 (MQ=255)                                      cAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGataat                                                                                   >  2:830842/1‑139 (MQ=255)                                               tATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTg                                                                          >  2:991842/1‑139 (MQ=255)                                                 tCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCa                                                                        >  2:308112/1‑139 (MQ=255)                                                    tCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAAtt                                                                     >  2:908189/1‑139 (MQ=255)                                                      aaTGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCa                                                                                         >  1:566689/1‑117 (MQ=255)                                                      aaTGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCa                                                                                         <  2:566689/117‑1 (MQ=255)                                                      aaTGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTg                                                                   >  2:395299/1‑139 (MQ=255)                                                      aaTGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTg                                                                   >  2:990364/1‑139 (MQ=255)                                                      aaTGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTg                                                                   >  2:1023368/1‑139 (MQ=255)                                                      aaTGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTg                                                                   >  2:1025342/1‑139 (MQ=255)                                                           tGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGttt                                                              >  2:49422/1‑139 (MQ=255)                                                           tGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGtt                                                               >  1:290592/1‑138 (MQ=255)                                                           tGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGtt                                                               <  2:290592/138‑1 (MQ=255)                                                            gCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTttct                                                                                            >  1:768241/1‑108 (MQ=255)                                                            gCTGTCTCACGCGCTAAAGATAGTTTTCTGGGATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTttct                                                                                            <  2:768241/108‑1 (MQ=255)                                                                          tAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTcg                                                                                                                             <  2:65459/61‑1 (MQ=255)                                                                          tAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTcg                                                                                                                             >  1:65459/1‑61 (MQ=255)                                                                          tAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAg                                                                                        <  2:752534/98‑1 (MQ=255)                                                                          tAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAg                                                                                        >  1:752534/1‑98 (MQ=255)                                                                           aaaGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGAtt                                              <  1:395299/139‑1 (MQ=255)                                                                             aGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTa                                            >  1:771350/1‑139 (MQ=255)                                                                               aTAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAAt                                          <  1:49422/139‑1 (MQ=255)                                                                                   ttttCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAAt                                                                      <  1:51604/107‑1 (MQ=255)                                                                                   ttttCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAAt                                                                      >  2:51604/1‑107 (MQ=255)                                                                                    tttCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCg                                     <  1:990364/139‑1 (MQ=255)                                                                                    tttCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCg                                     >  2:151580/1‑139 (MQ=255)                                                                                      tCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTttct                                                                                            >  1:90662/1‑82 (MQ=255)                                                                                      tCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTttct                                                                                            <  2:90662/82‑1 (MQ=255)                                                                                      tCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGca                                   >  1:285476/1‑139 (MQ=255)                                                                                      tCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGca                                   >  1:622425/1‑139 (MQ=255)                                                                                         ggTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACAt                                <  2:285476/139‑1 (MQ=255)                                                                                                ggCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAatat                                                                                                     <  1:641016/63‑1 (MQ=255)                                                                                                ggCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAatat                                                                                                     >  2:641016/1‑63 (MQ=255)                                                                                                ggCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTttctt                                                                                           >  2:355189/1‑73 (MQ=255)                                                                                                ggCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTttctt                                                                                           <  1:355189/73‑1 (MQ=255)                                                                                                   gATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAAttt                      <  2:302717/139‑1 (MQ=255)                                                                                                     tatGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCa                    >  2:533120/1‑139 (MQ=255)                                                                                                             ttATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCa            <  1:1023368/139‑1 (MQ=255)                                                                                                             ttATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCa            <  2:622425/139‑1 (MQ=255)                                                                                                             ttATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCa            <  1:908189/139‑1 (MQ=255)                                                                                                             ttATCGAGATGCAGTCCACATTTTAGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCa            <  2:404705/139‑1 (MQ=255)                                                                                                               aTCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCa                                                                                         <  2:628915/60‑1 (MQ=255)                                                                                                               aTCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCa                                                                                         >  1:628915/1‑60 (MQ=255)                                                                                                                      tGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCa                    >  1:313556/1‑122 (MQ=255)                                                                                                                      tGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCa                    <  2:313556/122‑1 (MQ=255)                                                                                                                       gCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCATGGTGTGGag  <  1:308112/139‑1 (MQ=255)                                                                                                                           |                                                                                                                                       TCTACTCAAAACATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCATGGTGTGGAG  >  NC_000913/4535319‑4535575

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑