Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,439,845	0	T	A	21.7%	154.3 / 41.8	69	intergenic (+52/+27)	ytfK/ytfL	DUF1107 family protein/UPF0053 family inner membrane protein
Reads supporting (aligned to +/- strand):  ref base T (26/28);  new base A (9/6);  total (35/34)
Fisher's exact test for biased strand distribution p-value = 5.61e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.79e-01

TCCGAAGTTAACCGTCAGGTTATGCGTCTGCAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCGAAAGGGCGGTGGCCTTGCTGTCGATC  >  NC_000913/4439746‑4439944                                                                                                    |                                                                                                    tCCGAAGTTAACCGTCAGGTTATGCGTCTGCAAACAGAGATGGCCTAACCAAAGTGCTATGCAGTAAAAAGTACTATGCATTAATAAGACGTCTCCTGAt                                                                                                     >  1:293567/1‑100 (MQ=255)   cGAAGTTAACCGTCAGGTTATGCGTCTGCAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGATTc                                                                                                   <  1:1204089/100‑1 (MQ=255)   cGAAGTTAACCGTCAGGTTATGCGTCTGCAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGAATc                                                                                                   <  1:1384333/100‑1 (MQ=255)     aaGTTAACCGTCAGGTTATGCGTCTGCAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGATTCAg                                                                                                 <  1:752127/100‑1 (MQ=255)      aGTTAACCGTCAGGTTATGCGTCTGCAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGTCGGCTCCTGATTCAgg                                                                                                <  1:138728/100‑1 (MQ=255)      aGTTAACCGTCAGGTTATGCGTCTGCAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGATTCAgg                                                                                                >  2:880242/1‑100 (MQ=255)      aGTTAACCGTCAGGTTATGCGTCTGCAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGATTCAgg                                                                                                <  1:350423/100‑1 (MQ=255)       gTTAACCGTCAGGTTATGCGTCTGCAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGATTCAGGa                                                                                               >  2:15480/1‑100 (MQ=255)        ttAACCGTCAGGTTATGCGTCTGCAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGATTCAGGAg                                                                                              <  2:1445204/100‑1 (MQ=255)         tAACCGTCAGGTTATGCGTCTGCAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATTCAGTAATAAGACGGCTCCTGATTCAGGatc                                                                                             <  1:866892/100‑3 (MQ=255)          aaCCGTCAGGTTATGCGTCTGCAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGATTCAGGAGcc                                                                                            >  2:1117457/1‑100 (MQ=255)           aCCGTCAGGTTATGCGTCTGCAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGAATCAGGAGCCg                                                                                           <  2:1452672/100‑1 (MQ=255)            ccgccAGGTTATGCGTCTGCAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGAATCAGGAGCCGt                                                                                          <  1:995735/96‑1 (MQ=255)             cGTCAGGTTATGCGTCTGCAAACAGAGACGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGAATCAGGAGCCGtc                                                                                         <  1:279331/100‑2 (MQ=255)              gTCAGGTTATGCGTCTGTAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGATTCAGGAGCCGtt                                                                                         <  1:212750/99‑1 (MQ=255)              gTCAGGTTATGCGTCTGCAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGATTCAGGAGCCGTTg                                                                                        <  1:593188/100‑1 (MQ=255)              gTCAGGTTATGCGTCTGCAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGATTCAGGAGCCGTTg                                                                                        <  1:554961/100‑1 (MQ=255)               tCAGGTTATGCGTCTGCAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGATTCAGGAGCCGTTGa                                                                                       <  2:293570/100‑1 (MQ=255)                 aGGTTATGCGTCTGCAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGATTCAGGAGCCGTTGATg                                                                                     <  2:1075386/100‑1 (MQ=255)                   gTTATGCGTCTGCAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGATTCAGGAGCCGTTGATGtt                                                                                   >  2:698599/1‑100 (MQ=255)                         cGTCTGCAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTggg                                                                             <  2:198584/100‑1 (MQ=255)                          gTCTGCAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTgggg                                                                            <  2:1063214/100‑1 (MQ=255)                             tGCAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGtt                                                                         >  2:389400/1‑100 (MQ=255)                               cAAACAGAGATGGCGTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTAc                                                                       >  1:831825/1‑100 (MQ=255)                                  aCAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTAcgcg                                                                    <  1:242845/100‑1 (MQ=255)                                          ggCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTttc                                                            >  1:1138784/1‑100 (MQ=255)                                          ggCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCCCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTttc                                                            >  1:109159/1‑100 (MQ=255)                                               aaCCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTcttctt                                                       >  1:116747/1‑100 (MQ=255)                                                aCCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTtcttt                                                      <  2:642551/100‑1 (MQ=255)                                                 ccAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTtcttta                                                     >  1:207646/1‑100 (MQ=255)                                                   aaagtgctatgcagtaaaaagtgctatgcagtaaTAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTtctttatc                                                   >  1:1177015/1‑100 (MQ=255)                                                    aagtgctatgcagtaaaaagtgctatgcagtaaTAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTtctttatct                                                  >  2:1168523/1‑100 (MQ=255)                                                       tgctatgcagtaaaaagtgctatgcagtaaTAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTtctttatcttta                                               <  2:1459017/100‑1 (MQ=255)                                                         ctatgcagtaaaaagtgctatgcagtaaTAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGc                                             >  1:1155025/1‑100 (MQ=255)                                                          tatgcagtaaaaagtgctatgcagtaaTAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCg                                            >  1:569628/1‑100 (MQ=255)                                                          tatgcagtaaaaagtgctatgcagtaaTAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCg                                            <  1:15479/100‑1 (MQ=255)                                                           atgcagtaaaaagtgctatgcagtaaTAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGt                                           >  2:1064658/1‑100 (MQ=255)                                                              cagtaaaaagtgctatgcagtaaTAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTGCTTGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCa                                         >  1:1121913/1‑99 (MQ=255)                                                               agtaaaaagtgctatgcagtaaTAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAgg                                       <  2:116749/100‑1 (MQ=255)                                                                gtaaaaagtgctatgcagtaaTAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGc                                      >  1:652978/1‑100 (MQ=255)                                                                gtaaaaagtgctatgcagtaaTAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGc                                      >  2:288254/1‑100 (MQ=255)                                                                gtaaaaagtgctatgcagtaaTAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGc                                      <  1:1538158/100‑1 (MQ=255)                                                                 taaaaagtgctatgcagtaaTAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCTACGCTTTCTTCTTTATCTTTAGCGTCAGGCa                                     <  2:1119943/100‑1 (MQ=255)                                                                  aaaaagtgctatgcagtaaTAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAg                                    <  2:1171128/100‑1 (MQ=255)                                                                   aaaagtgctatgcagtaaTAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGt                                   >  1:720650/1‑100 (MQ=255)                                                                     aagtgctatgcagtaaTAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGttt                                 >  2:1469167/1‑100 (MQ=255)                                                                          ctatgcagtaaTAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCg                            <  2:973923/100‑1 (MQ=255)                                                                          ctatgcagtaaTAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCg                            >  2:459713/1‑100 (MQ=255)                                                                          ctatgcagtaaTAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCg                            >  1:1176221/1‑100 (MQ=255)                                                                           tatgcagtaaTAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCGa                           >  1:191718/1‑100 (MQ=255)                                                                             tgcagtaaTAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCGaaa                         >  1:1145355/1‑100 (MQ=255)                                                                                    tatcaaCGGCTCCTGAATCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCGAAAGGGCGGt                  <  1:427006/95‑1 (MQ=255)                                                                                     taaGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCGAAAGGGCGGTg                 <  1:337151/100‑1 (MQ=255)                                                                                     atcaaCGGCTCCTGAATCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCGAAAGGGCGGta                 >  2:427010/5‑99 (MQ=255)                                                                                       caaCGGCTCCTGAATCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCGAACGGGCGGTGGc               >  1:1045723/3‑100 (MQ=255)                                                                                        aaCGGCTCCTGAATCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCGAAAGGGCGGTGGcc              >  1:1255086/2‑100 (MQ=255)                                                                                         aCGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCGAAAGGGCGGTGGCCt             <  1:1064647/100‑1 (MQ=255)                                                                                         aCGGCTCCTGAATCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCGAAAGGGCGGTGGCCt             >  2:1012667/1‑100 (MQ=255)                                                                                         aCGGCTCCTGAATCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCGAAAGGGCGGTGGCCt             >  2:469722/1‑100 (MQ=255)                                                                                         aCGGCTCCTGAATCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCGAAAGGGCGGTGGCCt             >  2:1012369/1‑100 (MQ=255)                                                                                         aCGGCTCCTGAATCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCGAAAGGGCGGTGGCCt             >  2:1302855/1‑100 (MQ=255)                                                                                          cGGCTCCTGAATCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCGAAAGGGCGGTGGCCtt            >  2:305849/1‑100 (MQ=255)                                                                                            gCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCGAAAGGGCGGTGGCCTTGc          <  1:256333/100‑1 (MQ=255)                                                                                            gCTCCTGAATCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCGAAAGGGCGGTGGCCTTGc          >  1:521140/1‑100 (MQ=255)                                                                                              tCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCGAAAGGGCGGTGGCCTTGCTg        <  2:428580/100‑1 (MQ=255)                                                                                               ccTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCGAAAGGGCGGTGGCCTTGCTGt       >  1:1001617/1‑100 (MQ=255)                                                                                                cTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCGAAAGGGCGGTGGCCTTGCTGTc      <  1:880720/100‑1 (MQ=255)                                                                                                cTGATTCAGGAGCCGTTGATGTTTCTGGGGGTAACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCGAAAGGGCGGTGGCCTTGCTGTc      >  2:1517078/1‑100 (MQ=255)                                                                                                cTGAATCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCGAAAGGGCGGTGGCCTTGCTGTc      <  2:1255100/100‑1 (MQ=255)                                                                                                   aTTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCGAAAGGGCGGTGGCCTTGCTGTCGAt   <  1:195077/100‑1 (MQ=255)                                                                                                    ttCAGGAGCCGTTTATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCGAAAGGGCGGTGGCCTTGCTGTCGATc  <  2:754178/100‑1 (MQ=255)                                                                                                    |                                                                                                    TCCGAAGTTAACCGTCAGGTTATGCGTCTGCAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATGCAGTAATAAGACGGCTCCTGATTCAGGAGCCGTTGATGTTTCTGGGGGTTACGCGACGCTTTCTTCTTTATCTTTAGCGTCAGGCAGTTTTGGCGAAAGGGCGGTGGCCTTGCTGTCGATC  >  NC_000913/4439746‑4439944

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑