Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,583,454	G→A	intergenic (+36/‑29)	yrhA → / → insA	pseudogene, interrupted by IS1E/IS1 repressor TnpA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,583,454	0	G	A	100.0%	139.5 / NA	45	intergenic (+36/‑29)	yrhA/insA	pseudogene, interrupted by IS1E/IS1 repressor TnpA
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (23/22);  total (23/22)

AATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAG  >  NC_000913/3583326‑3583550                                                                                                                                 |                                                                                                 aaTGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATgg                                                                                        <  2:1611748/139‑1 (MQ=255)           ataGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAg                                                                              <  2:791765/139‑1 (MQ=255)                         gatTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCt                                                                >  1:902085/1‑139 (MQ=255)                         gatTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCACCAGTGGCt                                                                >  1:984736/1‑139 (MQ=255)                                       tGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCt                                                             >  1:1119011/1‑128 (MQ=255)                                       tGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCt                                                             <  2:1119011/128‑1 (MQ=255)                                        gATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGc                                                 >  2:1617801/1‑139 (MQ=255)                                         aTCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTg                                                            <  2:591334/127‑1 (MQ=255)                                         aTCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTg                                                            >  1:591334/1‑127 (MQ=255)                                           cTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGt                                              <  2:984736/139‑1 (MQ=255)                                                   aCGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCtt                                                               >  1:547587/1‑114 (MQ=255)                                                   aCGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCtt                                                               <  2:547587/114‑1 (MQ=255)                                                   aCGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTg                                      >  2:329275/1‑139 (MQ=255)                                                   aCGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTg                                      >  2:1411467/1‑139 (MQ=255)                                                      gTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTc                                   >  2:1567051/1‑139 (MQ=255)                                                      gTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTc                                   >  2:1133991/1‑139 (MQ=255)                                                                 gggATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTccc                                           <  1:1010225/120‑1 (MQ=255)                                                                 gggATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACg                        <  2:902085/139‑1 (MQ=255)                                                                 gggATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGATTCTATCAGCTGTccc                                           >  2:1010225/1‑120 (MQ=255)                                                                   gATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACggg                      <  1:329275/139‑1 (MQ=255)                                                                    aTTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACgggg                     <  1:1617801/139‑1 (MQ=255)                                                                      tataGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGggtg                   <  1:1133991/139‑1 (MQ=255)                                                                       ataGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACggg                      >  2:1642239/1‑135 (MQ=255)                                                                       ataGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACggg                      <  1:1642239/135‑1 (MQ=255)                                                                         aGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGgtggtg                >  2:24419/1‑139 (MQ=255)                                                                             tttCAATATTTACTTATGACATTAAAGGCGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTa            >  2:281421/1‑139 (MQ=255)                                                                              ttCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGgt                                                                                       <  1:581370/63‑1 (MQ=255)                                                                              ttCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGgt                                                                                       >  2:581370/1‑63 (MQ=255)                                                                              ttCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAg                                 <  1:630235/117‑1 (MQ=255)                                                                              ttCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAg                                 >  2:630235/1‑117 (MQ=255)                                                                                cAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCt                               >  2:113352/1‑117 (MQ=255)                                                                                cAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCt                               <  1:113352/117‑1 (MQ=255)                                                                                       tACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTCTTTTTGAGGTGCTCCAGTGGATTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAg  <  1:1411467/139‑1 (MQ=255)                                                                                        aCTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCtt                                                               <  1:381010/77‑1 (MQ=255)                                                                                        aCTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCtt                                                               >  2:381010/1‑77 (MQ=255)                                                                                        aCTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGt                                              <  1:848827/94‑1 (MQ=255)                                                                                        aCTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGt                                              >  2:848827/1‑94 (MQ=255)                                                                                           tATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCaa     <  2:634695/132‑1 (MQ=255)                                                                                           tATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCaa     >  1:634695/1‑132 (MQ=255)                                                                                             tGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAgg                                                                             <  1:683746/58‑1 (MQ=255)                                                                                             tGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAgg                                                                             >  2:683746/1‑58 (MQ=255)                                                                                               aCATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACgggg                     <  2:1120972/112‑1 (MQ=37)                                                                                               aCATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACgggg                     >  1:1120972/1‑112 (MQ=37)                                                                                               aCATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGggt                    >  1:1285210/1‑113 (MQ=37)                                                                                               aCATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGggt                    <  2:1285210/113‑1 (MQ=37)                                                                                                                                 |                                                                                                 AATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAG  >  NC_000913/3583326‑3583550

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: ‑