Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,650,640	T→C	pseudogene (563/921 nt)	ydfE →	Qin prophage; protein YdfE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,650,640	0	T	C	100.0%	153.7 / NA	44	pseudogene (563/921 nt)	ydfE	Qin prophage; protein YdfE
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (25/19);  total (25/19)

CAACATTCGACGGACATATCGTTGAAGCGTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAATTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAATACACGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCAACAGGAAAAATCAGC  >  NC_000913/1650508‑1650776                                                                                                                                     |                                                                                                                                         cAACATTCGACGGACATATCGTTGAAGCGTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCa                                                                                                                                   <  2:121342/140‑1 (MQ=255)     aTTCGACGGACATATCGTTGAAGCGTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAgaga                                                                                                                               >  2:265918/1‑140 (MQ=255)                 tatCGTTGAAGCGTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGa                                                                                                                   >  2:315059/1‑140 (MQ=255)                      ttGAAGCGTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGaaaaaa                                                                                                              <  2:227487/140‑1 (MQ=255)                        gAAGCGTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGGAACTCAGGCAGAGATGCGCATCTGGAAAAAACg                                                                                                            >  1:426600/1‑140 (MQ=255)                        gAAGCGTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACg                                                                                                            >  1:319824/1‑140 (MQ=255)                        gAAGCGTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACg                                                                                                            >  1:407830/1‑140 (MQ=255)                         aaGCGTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGt                                                                                                           >  1:385808/1‑140 (MQ=255)                             gTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTcgcg                                                                                                       <  2:296358/140‑1 (MQ=255)                              ttGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGa                                                                                                      >  1:333879/1‑140 (MQ=255)                                 atgaAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAgg                                                                                                   >  2:360236/1‑140 (MQ=255)                                  tgaAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGGAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGt                                                                                                  <  2:426600/140‑1 (MQ=255)                                  tgaAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAACCGTCGAGAAGGt                                                                                                  <  2:332170/140‑1 (MQ=255)                                  tgaAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGt                                                                                                  <  1:130439/140‑1 (MQ=255)                                   gaAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTg                                                                                                 <  2:61449/140‑1 (MQ=255)                                     aaaTGCCAGAAGTTCACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGaa                                                                                               <  2:333879/140‑1 (MQ=255)                                              aaGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGaa                                                                                      >  1:16560/1‑140 (MQ=255)                                                gTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAAc                                                                                    >  2:39081/1‑140 (MQ=255)                                                    aCGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGa                                                                                <  2:16560/140‑1 (MQ=255)                                                        cATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAAt                                                                            >  2:152393/1‑140 (MQ=255)                                                              tCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAATACACGt                                                                      <  1:489185/140‑1 (MQ=255)                                                                   aGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAATACACGTCtgtt                                                                 >  2:136847/1‑140 (MQ=255)                                                                     cTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAATACACGTCtgttgt                                                               >  1:477344/1‑140 (MQ=255)                                                                               aCGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAATACACGTCTGTTGTTGATCTCGcc                                                     >  2:277117/1‑140 (MQ=255)                                                                               aCGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAATACACGTCTGTTGTTGATCTCGcc                                                     <  1:136847/140‑1 (MQ=255)                                                                                cGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAGACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAATACACGTCTGTTGTTGATCTCGcc                                                     <  1:525353/139‑1 (MQ=255)                                                                                cGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAGACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAATACACGTCTGTTGTTGATCTCGcc                                                     >  2:525353/1‑139 (MQ=255)                                                                                      tgggtgggTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAATACACGTCTGTTGTTGATCTCGCCCGCGCCa                                              >  1:76394/1‑140 (MQ=255)                                                                                         gtgggtTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAATACACGTCTGTTGTTGATCTCGCCCGCGCCagag                                           <  1:39081/140‑1 (MQ=255)                                                                                            ggtTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAATACACGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCa                                        <  1:315059/140‑1 (MQ=255)                                                                                             gtTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAATACACGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCaa                                       >  1:16835/1‑140 (MQ=255)                                                                                              ttAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAATACACGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAAt                                      <  2:167298/140‑1 (MQ=255)                                                                                              ttAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAATACACGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAAt                                      <  1:340891/140‑1 (MQ=255)                                                                                                       aaTGTATTCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAATACACGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAATCAACAGTac                             >  1:545429/1‑140 (MQ=255)                                                                                                             ttCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAATACACGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGaa                       >  2:166662/1‑140 (MQ=255)                                                                                                             ttCCTGGTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAATACACGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGaa                       >  2:422147/1‑140 (MQ=255)                                                                                                                   gTGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAATACACGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCa                 >  1:538715/1‑140 (MQ=255)                                                                                                                    tGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAATACACGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCaa                >  2:12509/1‑140 (MQ=255)                                                                                                                    tGCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAATACACGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCaa                <  1:360236/140‑1 (MQ=255)                                                                                                                     gCTAAATGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAATACACGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCAAc               >  2:23023/1‑140 (MQ=255)                                                                                                                         aaTGGCCCGAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGACGCGAAGGTGAAGGCAAGGAAACCGGAAAATACACGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCAACAGGa           >  1:247242/1‑140 (MQ=255)                                                                                                                                 gAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAATACACGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCAACAGGAAAAATCAg   <  2:76394/140‑1 (MQ=255)                                                                                                                                 gAAACTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAATACACGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCAACAGGAAAAATCAg   >  1:350291/1‑140 (MQ=255)                                                                                                                                  aaaCTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAATACACGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCAACAGGAAAAATCAGc  <  1:166662/140‑1 (MQ=255)                                                                                                                                  aaaCTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAATACACGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCAACAGGAAAAATCAGc  <  1:152393/140‑1 (MQ=255)                                                                                                                                     |                                                                                                                                         CAACATTCGACGGACATATCGTTGAAGCGTTGATGAAAATGCCAGAAGTTAACGCCATGTATCCGGAGCTTAAGTTGCACGCCATTGGGTGGGTTAAGCATAAATGTATTCCTGGTGCTAAATGGCCCGAAATTCAGGCAGAGATGCGCATCTGGAAAAAACGTCGCGAAGGTGAACGCAAGGAAACCGGAAAATACACGTCTGTTGTTGATCTCGCCCGCGCCAGAGCCAATCAACAGTACACTGAAAATTCAACAGGAAAAATCAGC  >  NC_000913/1650508‑1650776

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑