Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,222,233	0	G	A	44.9%	51.1 / 27.2	49	pseudogene (60/75 nt)	ycgH	pseudogene; putative ATP‑binding component of a transport system
Reads supporting (aligned to +/- strand):  ref base G (22/5);  new base A (0/22);  total (22/27)
Fisher's exact test for biased strand distribution p-value = 1.64e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAAAGTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGC‑TACAATGACACCGCAGTGATGGTGGGCCTG‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAGCGCAAACCTG  >  NC_000913/1222087‑1222382                                                                                                                                                    |                                                                                                                                                       gAAAGTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGC‑TACAATGACACCGCAGTGATGGTGGGCCTG‑aaa                                                                                                                                                    <  2:1021066/150‑1 (MQ=255) gAAAGTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGC‑TACAATGACACCGCAGTGATGGTGGGCCTG‑AAat                                                                                                                                                   >  1:639131/1‑151 (MQ=255)    aGTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGC‑TACAATGACACCGCAGTGATGGTGGGCCTG‑AAatat                                                                                                                                                 >  2:325638/1‑150 (MQ=255)           cAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGC‑TACAATGACACCGCAGTGATGGTGGGCCTG‑AAATATAAGTTCTg                                                                                                                                         <  1:332079/151‑1 (MQ=255)           cAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGC‑TACAATGACACCGCAGTGATGGTGGGCCTG‑AAATATAAGTTCTg                                                                                                                                         <  1:728917/151‑1 (MQ=255)             aGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGC‑TACAATGACACCGCAGTGATGGTGGGCCTG‑AAATATAAGTTCTGAt                                                                                                                                       >  2:717673/1‑151 (MQ=255)              gATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGC‑TACAATGACACCGCAGTGATGGTGGGCCTG‑AAATATAAGTTCTGATc                                                                                                                                      >  2:780897/1‑151 (MQ=255)                       aGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGC‑TACAATGACACCGCAGTGATGGTGGGCCTG‑AAATATAAGTTCTGATCCCGCCGtt                                                                                                                              >  1:528719/1‑150 (MQ=255)                           aTTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGC‑TACAATGACACCGCAGTGATGGTGGGCCTG‑AAATATAAGTTCTGATCCCGCCGTTAGCt                                                                                                                          >  2:622553/1‑150 (MQ=255)                                    aaaTTAAACTGGGCGAAAAGGGCACCCTGAACCCGGCGGCCAGCGTCGGGGGAAGGGGGGCGTGCGGGGGGGTGATAATGGC‑TAAAATGACCCCGCAGTGAGGGTGGGCCTA‑AAATATAATTTCTGATCCCGCCGTTAGCTAAAAAAcc                                                                                                                  <  1:346306/149‑1 (MQ=255)                                         aatctgggggaaaaTGGCACCCTGAACCCGGGGGCCGGCGGGGGGGGAATGTGGGCGTGCGGCGGGTTAATAATGGC‑TACAATGACCCCGAGTTAATGGGGGGCCTA‑AAATATAGGTTCTGATCCCGCCGTTAGCTAAAAAACCGcgtcgt                                                                                                           <  2:273578/140‑1 (MQ=255)                                                gCGAAAAGGGCACCCTGACGCCAGCGCCCAGCGTCGGGGGAAGGTGGGCGTGCAGGTGGGTGATAAGGGC‑TACAATCACCCCGAGGTGATGGGGGGCTTA‑AAATAAAAGTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTAtt                                                                                                        <  2:43670/147‑1 (MQ=255)                                                  gTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGC‑TACAATGACACCGCAGTGATGGTGGACCTG‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCg                                                                                                   >  2:424630/1‑150 (MQ=255)                                                    aaaTGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGC‑TACAATGACACCGCAGTGATGGTGGGCCTG‑AAATATAAGTTCTGATCCCGACGTTAGCTAAAAAACCGCGTCGTATTCATCGa                                                                                                  >  2:266/1‑149 (MQ=255)                                                    aaaGGGCACCCTGAACCCAGGGGCCAGCGTGGGGGGAGTGGGGGCGTGCGGCGGGGTAATAATGGC‑TACAGTGCCCCCGAAGTGATGGGGGGCGTA‑AAATATATTTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGa                                                                                                  <  2:135314/149‑1 (MQ=255)                                                        ggaacccTGAACCCAGCGGCCAGCGTGTGGGGATTGTGGGCGTGCAGTTGGGTGATAATGGC‑TACAATGACCCCGCAGTGATGGGGGGCCTA‑AAATATAAGTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCgg                                                                                             <  1:263169/145‑1 (MQ=255)                                                           aaCCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGC‑TACAATGACACCGCAGTGATGGTGGGCCTG‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTAc                                                                                          >  1:918353/1‑150 (MQ=255)                                                           aaCCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGC‑TACAATGACACCGCAGTGATGGTGGGCCTG‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTAc                                                                                          >  1:595634/1‑150 (MQ=255)                                                                   tCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGC‑TACAATGACACCGCAGTGATGGTGGGCCTG‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAat                                                                                 >  2:993635/1‑151 (MQ=255)                                                                    ccAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGC‑TACAATGACACCGCAGTGATGGTGGGCCTG‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAat                                                                                 >  2:847918/1‑150 (MQ=255)                                                                         ggCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGTC‑TAAAATGACCCCGCAGTGAGGGTGGGCATA‑AAATATAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAAtattat                                                                            <  1:406866/150‑1 (MQ=255)                                                                         gcccAGCGTCGGGGGAATGTGGGGGTGCAGCTGGGTGATAAGGGC‑TACAATGCCCCCGCGGTGAGGGTGGGCCTA‑AAATATAAGTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATattatt                                                                           <  1:215386/149‑1 (MQ=255)                                                                            cAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGC‑TACAATGACACCGCAGTGATGGTGGGCCTG‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTAttttt                                                                        >  1:527805/1‑151 (MQ=255)                                                                             aGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGC‑TACAATGACACCGCAGTGATGGTGGGCCTG‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTAtttttt                                                                       >  2:382647/1‑151 (MQ=255)                                                                              gcttCTGGGGATTGTGGGCGTCCGGGTGGGTGATAATGGC‑TACAAACCCCCCGCAGTGATGGT‑GGCCTGAAAATAAAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTAtttttt                                                                       <  1:196452/147‑1 (MQ=255)                                                                                    ggggAGGGTGGGGGGGCGGCGGGGTAATAATGGC‑TAAAAGGACACCGAAGGGGTGGTGGGCAAA‑AAAAATAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATa                                                                <  2:639097/151‑1 (MQ=255)                                                                                           gtgGGCGTGCAGGTGGGTGATAATGGC‑TAAAATGCCCCCGCAGTGAGGGGGGGCTTA‑AAATATAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACg                                                           <  1:982633/149‑1 (MQ=255)                                                                                             gggCGTGCAGCGGGGTGA‑AAGGGCTTAAAATGACCCCGAAGTGGTGGTGGGCCTG‑AATTATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCAt                                                        <  1:984511/150‑1 (MQ=255)                                                                                                 gTGCAGCTGGTAGATAATGGC‑AAAAAGGACCCCGCAGGGATGGGGGGCTTA‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGgtg                                                    <  1:865484/150‑1 (MQ=255)                                                                                                    cAGCGGGGTAATAATGCC‑TACAATGCCCCCGAAGTGAGGGTGGGCCTA‑AAATATAATTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGgt                                                     <  1:669935/146‑1 (MQ=255)                                                                                                        tGGGTGATAATGGC‑TACAATGACACCGCAGTGATGGTGGGCCTG‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAAt                                            >  1:416991/1‑151 (MQ=255)                                                                                                              aTAATGGC‑TACAATGACACCGCAGTGATGGTGGGCCTG‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGt                                      >  2:663337/1‑151 (MQ=255)                                                                                                              aTAATGAC‑AACAAGGACACGGCAGTGATGGGGGGCAAA‑AAATAAAGGTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGc                                         <  2:275575/148‑1 (MQ=255)                                                                                                                aagggC‑TAAAGTGCCACCGCAGTGAGGGGGGGCTTA‑AAATATAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGcc                                        <  1:630438/144‑1 (MQ=255)                                                                                                                 attgaataaaaTGACCCCGCAGGGAGGGTGGGTCTA‑AAAAATAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAAt                                            <  2:335213/134‑1 (MQ=255)                                                                                                                   gggttaaaaTGACCCCGCAGTGAGGGGGGGCCTA‑AAATATAATTTCTGCTCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGAt                                   <  1:666078/143‑1 (MQ=255)                                                                                                                   gggttaaaaTGACCCCGAAGAGATGGGGGGCCTA‑AAATATAGTTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGAt                                   <  2:923337/143‑1 (MQ=255)                                                                                                                          aacaaccccGGAGTGATGGTGGGACTA‑AAATATAATTTGTGATTCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAg                             <  2:821420/142‑1 (MQ=255)                                                                                                                           aTGACCCCGCAGTGATGGGGGGCGTA‑AAATATAATTTTTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCAt                          <  1:569327/151‑1 (MQ=255)                                                                                                                              accccgaagttttggtggGCTTA‑AAATATATTTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCAttt                        <  1:780933/138‑1 (MQ=255)                                                                                                                               cacCGCAGTGTTGGGGGCCCAA‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCAttt                        <  1:294761/149‑1 (MQ=255)                                                                                                                               cacCGCAGTGATGGTGGGCCTG‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGc                      >  2:364525/1‑151 (MQ=255)                                                                                                                                  cGCAGTGATGGTGGGCCTA‑AAATATAAGTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCg                     <  2:947636/149‑1 (MQ=255)                                                                                                                                     aGTGATGGTGGGCCTG‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCt                >  2:141350/1‑151 (MQ=255)                                                                                                                                     aGTGATGGTGGGCCTG‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCt                >  1:786055/1‑151 (MQ=255)                                                                                                                                         aTGGTGGGCCTG‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCttt              >  1:951278/1‑149 (MQ=255)                                                                                                                                         aTGGTGGGCCTG‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCttt              >  1:461081/1‑149 (MQ=255)                                                                                                                                         aTGGTGGGCCTG‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCtt               >  2:572404/1‑148 (MQ=255)                                                                                                                                              gggCCTA‑AAATAAAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAGCGCa        <  1:770565/150‑1 (MQ=255)                                                                                                                                                    g‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAGCGCAAACCTg  >  2:201994/1‑150 (MQ=255)                                                                                                                                                    |                                                                                                                                                       GAAAGTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGC‑TACAATGACACCGCAGTGATGGTGGGCCTG‑AAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAGCGCAAACCTG  >  NC_000913/1222087‑1222382

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑