Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,097,581	0	A	G	40.0%	80.8 / 16.3	50	noncoding (72/88 nt)	serX	tRNA‑Ser
Reads supporting (aligned to +/- strand):  ref base A (7/23);  new base G (20/0);  total (27/23)
Fisher's exact test for biased strand distribution p-value = 2.40e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTG‑CCGTATACAC‑ACTTT‑CCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAAT‑TGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGAA  >  NC_000913/1097436‑1097728                                                                                                                                                  |                                                                                                                                                        cACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTc                                                                                                                                                      <  2:1071170/149‑1 (MQ=11)       gTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAAccccc                                                                                                                                              <  2:652629/151‑1 (MQ=35)        ttCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATCGAAccccc                                                                                                                                              >  1:878998/1‑150 (MQ=18)          cACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGa                                                                                                                                            <  2:26322/150‑1 (MQ=38)           aCGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATa                                                                                                                                          <  1:835858/151‑1 (MQ=39)              gTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGGTCGAAccccccct                                                                                                                                           >  2:424438/1‑144 (MQ=16)                    ccAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTG‑CCGt                                                                                                                                <  1:579633/151‑1 (MQ=255)                           gCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTG‑CCGTATacac‑a                                                                                                                        <  1:648054/151‑1 (MQ=255)                                   cAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCGAAACCCCCCTACGTTG‑CCGCATACAC‑ACttt                                                                                                                    >  2:444565/1‑147 (MQ=255)                                     gTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTG‑CCGTATACAC‑ACTTT‑CCAGGc                                                                                                             <  2:155031/151‑1 (MQ=255)                                        gTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTG‑CCGTATACAC‑ACTTT‑CCAGGCGt                                                                                                           <  1:1093846/150‑1 (MQ=255)                                          cGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTTGCAACCCCCATACGTTG‑CCGTATACAC‑ACTTT‑TCCCGCGTggt                                                                                                        >  2:333858/1‑149 (MQ=14)                                                    tCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTATTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCGAAACCCCGATACGTTG‑CCGTATACAC‑ACTTT‑TCAGGCGTGCTCCTTCCGcc                                                                                               >  2:309595/1‑150 (MQ=255)                                                       gggCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGGTTGGACCCCCCGTATGTTG‑CCGTATAAAA‑ACTTT‑TCAGGCGGGGTCCTTCCGCCACTc                                                                                           >  1:942647/1‑151 (MQ=14)                                                       gggCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTG‑CCGTATACAC‑ACTTT‑CCAGGCGTGCTCCTTCAGCCACTc                                                                                           <  1:998126/151‑1 (MQ=255)                                                        ggCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCGAACCCCCGATACGTTG‑CCGTATACAC‑ACTTT‑CCCGGCGGGCTCCTTCAGcccc                                                                                             >  2:1096316/1‑146 (MQ=255)                                                           ttCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGGGGGGGGGGTTCGAACCCCCCCTACGTTT‑CCGTATAAAA‑ACTTT‑CCCGGCGGGCTCCTTcccccccccgg                                                                                         >  2:877385/1‑139 (MQ=17)                                                              tcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTTGGACCCCCCATACGTTG‑CCGTATAAAC‑ACTTT‑CCAGGCGGGCTCCTTCAGCCACCCGGACAcc                                                                                    >  2:496889/1‑151 (MQ=17)                                                              tcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCGAACCCCCCATACGTTT‑CCGTATACAC‑ACTTT‑CCAAGCGGGCTCCCTCAGCCCCCCCGACAcc                                                                                    >  2:474267/1‑151 (MQ=17)                                                                     cccGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGGGGGGGGGGTTCGAACCCCCGCAACATTGCCCGCTAAAAC‑ATTTT‑CC‑CGCGTGGTCCTTTAGCCAcccccgacactcccc                                                                               >  1:804436/1‑135 (MQ=2)                                                                          tgtgtgCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTG‑CCGTATACAC‑ACTTT‑CCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAAt‑t                                                                         <  1:40151/149‑1 (MQ=255)                                                                           gtgtgCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTG‑CCGTATACAC‑ACTTT‑CCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAAT‑TGt                                                                       <  2:1059147/150‑1 (MQ=255)                                                                                    ataCGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTG‑CCGTATACAC‑ACTTT‑CCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAAT‑TGTCGTTCCTGTc                                                             <  2:500035/151‑1 (MQ=255)                                                                                              aaaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTG‑CCGTATACAC‑ACTTT‑CCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAAT‑TGTCGTTCCTGTCTTGCTGGAAc                                                   <  1:167826/151‑1 (MQ=255)                                                                                                 gCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTG‑CCGTATACAC‑ACTTT‑CCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAAT‑TGTCGTTCCTGTCTTGCTGGAACggg                                                <  1:49698/151‑1 (MQ=255)                                                                                                    cGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGGGGCGGGGGGTTGGACACCCGGTTCGTTG‑CCGTCTACCCTCCTTTCCCGGGCGTGC‑CTTTCTCCCA‑TCGGACACCTCACAAAATATATC‑CTCCTGTCTTTCTGGGAAGGgcg                                              >  1:99814/1‑150 (MQ=2)                                                                                                       aCTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTTGTAACCCCCCTAAGTTT‑CCGTATAAAC‑ACTTT‑TCAGGGGGGCTCCTTCCGCCACCCGGGCACCCCCCCAAAA‑TTTTGTTCCTGTCTTTCTGGAACGGgcgc                                             >  1:144547/1‑148 (MQ=9)                                                                                                          ttCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCTGACCCCCGATAAGGTG‑GCGGATACAA‑ACTTT‑CCAGGCGTGCTCCTTCAGCCACTCCGAAAACCCCCCCAAA‑TGTTGTTCCTGTCTTTCTGGGAAGGGGGCCAAttt                                       >  2:476492/1‑151 (MQ=9)                                                                                                             gTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCGTAACCCCCATAAGTTT‑CCGTGTTCAC‑CCTTT‑CCAGGCGGGCGCCCTTAGCCCCCCGGGCCCCCCCCCCAAT‑TTTTGTTCCTGTTTTTCTGGGACGGGGGCTAAatt                                       >  1:775582/1‑148 (MQ=9)                                                                                                                cGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCGAACCCCCCCTACGTTT‑TCGTATACAC‑ACTTT‑TCCGGCGGGGTCCCTTAGCCCCCCCGGCACCCCCCCCAAT‑TTTCGTTCCCGTCTTTCTGGGACGGGCGCCAATTTTggg                                   >  1:555659/1‑149 (MQ=9)                                                                                                                cGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTG‑CCGTATACAC‑ACTTT‑CCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAAT‑TGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGaa                                 <  1:463832/151‑1 (MQ=255)                                                                                                                 gAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCGCACCCCCGATACGTTG‑CCGTATAAAC‑ACCTT‑TCAGGCGGGGCCCCTCAGCCACTCGGACACCCCACCCAAT‑TTTCGTTCCTGTCTTGTTTGAACGGGCGCTAATTTAagg                                   >  1:1041908/1‑148 (MQ=17)                                                                                                                  aGCTCTTCTTTAAATATGGCGGGGAGGGGGGGGTTCGAACCCCCCATACCTTT‑CCGTATAAAC‑ACCTT‑CCCGGCGGGCTCCTTCAGCCCCCCCGGCACCTCACCCAAA‑TTTCGTTCCTGTCTTGCTTGAACGGGCGCCAATTTTGGGgaa                                >  1:261087/1‑150 (MQ=12)                                                                                                                     tcttctTTAAATATGGCGGTGGGGGGGGGGGTCGGAACCCCCACACGTTT‑TCGTATACAC‑ACTTT‑CCCGGCGGGCTCCTTCAGCCACTCCGGCACCCCCCCCAAT‑TGTCGTTTCTGTCTTGCTGGGACGGGCGCCAATTTTTGGaaaaaa                             >  1:770173/1‑147 (MQ=12)                                                                                                                        tcttTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTG‑CCGTATACAC‑ACTTT‑CCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAAT‑TGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGa                          <  2:120659/150‑1 (MQ=255)                                                                                                                           ttAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTG‑CCGTATACAC‑ACTTT‑CCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAAT‑TGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGAcc                        <  2:12163/149‑1 (MQ=255)                                                                                                                           ttAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTG‑CCGTATACAC‑ACTTT‑CCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAAT‑TGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCt                       <  2:38823/150‑1 (MQ=255)                                                                                                                           ttAAATATGGCGGTGAGGGGGGGATTCGAACCCCCCATACGTTT‑GCGTATACAA‑ACTTT‑TCCGGCGGGGTCCTTCCGCCCCTCGGACACCCCCCCCAAA‑TGTTGGTCCTTTCTTTTTGGGACGGGCGCCAATTTTTGGAAATAATGAcc                        >  1:876535/1‑149 (MQ=9)                                                                                                                              aaTATGGCGGTGAGGGGGGGGTTTGAACCCCCCCTACGTTG‑CCGTATACAC‑AATTT‑TCAGGGGTGCTCCTTCAGCCACACCGACACCTCACCAAAA‑TTTTGTTTCTGTCTTGCTGGAACGGGCGCTTATTTTGGGAAATCAAGACCTGAgg                   >  1:608302/1‑151 (MQ=18)                                                                                                                              aaTATGGCGGTGAGGGGGGGGTTCGAACCCCCCATACGCTG‑CCGGATACAC‑ACTTT‑TCCGGCGGGCTCCCTTAGCCACCCCGACACCCCACCCAAT‑TGTTGTTCCTGTCTTTTTGGGAAAGGCGGCAATTTTTGGAAAAAATGACCTGAg                    >  1:428155/1‑150 (MQ=9)                                                                                                                               atatGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTG‑CCGTATACAC‑ACTTT‑CCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAAT‑TGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAgg                   >  2:175504/1‑150 (MQ=255)                                                                                                                               atatGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTG‑CCGTATACAC‑ACTTT‑CCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAAT‑TGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAgg                   >  1:229419/1‑150 (MQ=255)                                                                                                                               atatGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTG‑CCGTATACAC‑ACTTT‑CCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAAT‑TGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGt                  <  2:275100/151‑1 (MQ=255)                                                                                                                                     cGGTGAGGGGGGGATTCGAACCCCCGATACGTTG‑CCGTATACAC‑ACTTT‑CCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAAT‑TGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTcaacaa            <  1:226970/151‑1 (MQ=255)                                                                                                                                         gAGGGGGGGATTCGAACCCCCGATACGTTG‑CCGTATACAC‑ACTTT‑CCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAAT‑TGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACtt        >  1:6827/1‑151 (MQ=255)                                                                                                                                         gAGGGGGGGATTCGAACCCCCGATACGTTG‑CCGTATACAC‑ACTTT‑CCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAAT‑TGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACtt        <  1:574717/151‑1 (MQ=255)                                                                                                                                           gggggggATTCGAACCCCCGATACGTTG‑CCGTATACAC‑ACTTT‑CCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAAT‑TGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACtttt      >  1:253446/1‑151 (MQ=255)                                                                                                                                             gggggATTCGAACCCCCGATACGTTG‑CCGTATACAC‑ACTTT‑CCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAAT‑TGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTg    <  2:37701/151‑1 (MQ=255)                                                                                                                                               gggATTCGAACCCCCGATACGTTG‑CCGTATACAC‑ACTTT‑CCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAAT‑TGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGaa  <  2:283619/151‑1 (MQ=255)                                                                                                                                               gggATTCGAACCCCCGATACGTTG‑CCGTATACAC‑ACTTT‑CCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAAT‑TGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGa   >  1:1039698/1‑150 (MQ=255)                                                                                                                                                  |                                                                                                                                                        CACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTG‑CCGTATACAC‑ACTTT‑CCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAAT‑TGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACCTGAGGTCAACAAACTTTTTGAA  >  NC_000913/1097436‑1097728

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑