Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	987,522	0	C	A	45.0%	64.4 / 23.3	40	intergenic (‑540/+63)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
Reads supporting (aligned to +/- strand):  ref base C (6/16);  new base A (18/0);  total (24/16)
Fisher's exact test for biased strand distribution p-value = 1.48e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTGCAAATAGA‑TTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCACGCCAGTTACGTAAGCAATCAGACGTTC  >  NC_000913/987373‑987671                                                                                                                                                        |                                                                                                                                                      aTAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTGCAAATAGA‑TTGCTTGACTTaacaaaca                                                                                                                                                      <  2:408068/151‑1 (MQ=255)    gTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTGCAAATAGA‑TTGCTTGACTTtacaaacaaa                                                                                                                                                    >  1:714216/1‑148 (MQ=255)                tgCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTGCAAAAAAA‑TTGCTTTACTTAAAAAAAAGAAAAATTGACa                                                                                                                                          >  1:664287/1‑148 (MQ=255)                 gCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTGCAAATAGA‑TTGCTTGACTTAACAAACAGATAACTTGACAGaaa                                                                                                                                      <  2:366358/151‑1 (MQ=255)                   tATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTGGGAAAAGA‑TTTCTTGACTTTTAAAAAAAAAAAATTTACAGaaa                                                                                                                                      >  2:146547/1‑149 (MQ=255)                   tATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTGCAAAAAAA‑ATGCTTTACTTAACAAAAAAAAAACATTACAGaaaa                                                                                                                                     >  2:554163/1‑150 (MQ=255)                             gAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTGCAAATAGA‑TTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAag                                                                                                                          <  1:728028/151‑1 (MQ=255)                              aaaaaaCTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTGGAAATAAA‑CTTTTTGGCTTAAAAAACAGAAAAAATGGTAGAAAAAATaaaaaaa                                                                                                                           >  1:385075/1‑149 (MQ=255)                               aaaaaCTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGGGGCAATAAA‑ATTCTTTACTTTACAAAAAGAAAAATTTAGAGaaaaaaaaaaaaaaaa                                                                                                                         >  1:743498/1‑148 (MQ=255)                                  aaCTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTGCAAATAGA‑TTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCa                                                                                                                     <  2:396898/151‑1 (MQ=255)                                  aaCTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTGCAAATAGA‑ATTCTTTATTTTAAAAAAAAAAAAATTTACAGGAAAAATaaaaaaaaa                                                                                                                         >  1:145364/1‑145 (MQ=255)                                     tAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTGCGAAAAGG‑TTGGTTGGCTTTACAAAAAAATAAAATGAAAGaaaaaaaaaaaaaaaa                                                                                                                         >  1:287262/1‑142 (MQ=255)                                      aaTCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTGGAAAAAAA‑TTTGTTTTCTTTAAAAAAAAAAAAAATTACAGAAAAAAAAAAAAAAAAACCAGCgg                                                                                                                 >  1:499424/1‑151 (MQ=255)                                         ccGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTGGAAAAAAA‑ATGTTTTACTTAACAAAAAAAAAAAATGTAAGaaaaaaaaaaaaaaaaacaaacggg                                                                                                                >  2:680193/1‑138 (MQ=255)                                          cGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTGCAAAAAAA‑TTGCTTTTATTTAAAAAAAAAAAAATTTACAGAAAAGATaaaaaaaaaaaca                                                                                                                     >  2:450672/1‑137 (MQ=255)                                           gCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGGGAAAAAAA‑TGGTTTTACTT‑ACAAAAAAAAAAATTTGCAGaaaaaaaaaaaaaaaaaaaaaggg                                                                                                                 >  2:686369/1‑136 (MQ=255)                                            cAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTGGAAAAAAA‑TTTCTTTACTTTACAAAAAAATAAATTTACAGAAAAAATAAAAAAAAAAACAGCggg                                                                                                                >  1:442492/1‑146 (MQ=255)                                             aaTAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTGCAAATAAA‑ATGGTTTGTTTAACAAAAAAAAAAATTTACAGAAAAAAAAAAAAAAAAAACAGCGGgcg                                                                                                              >  2:580541/1‑147 (MQ=255)                                               tAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTGGAAAAAAATTTTTTTTATTTAAAAAAAAAAAAATTTGA‑AGAAAAAATAAAAAAAAAAACAGCgggggggg                                                                                                           >  2:840597/1‑143 (MQ=255)                                                aaGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTGCAAATAGA‑TTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGct                                                                                                        <  1:304198/150‑1 (MQ=255)                                                                     cgcgTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTGCAAAAAAA‑TTTCTTCGGTTAACAAAAAAAAAAACTTACAAGAAACATAAAAAAAAAACCACCGGGCGATGGGCCCTGAAGAAGCAAAATTaaaa                                                                                   >  1:639453/1‑150 (MQ=255)                                                                        gTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTGCAAATAGA‑TTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTg                                                                               <  1:557920/151‑1 (MQ=255)                                                                        gTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTGCAAATAGA‑TTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTg                                                                               <  2:219528/151‑1 (MQ=255)                                                                         tAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTGGAAAAAAA‑TTTCTTGGATTAACAAAAAGAAAACTTTACAGAAAAAAAAAAAAAAAAACCAGCGGGGGCTGGGTCTTGTAGACGCTAAAATAGaaacagg                                                                              >  1:443355/1‑146 (MQ=255)                                                                          aaaTGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTGCAAATAGA‑TTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGc                                                                             <  1:653733/151‑1 (MQ=255)                                                                              gTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTGCAAATAGA‑TTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGtt                                                                          <  1:107228/150‑1 (MQ=255)                                                                               ttGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTGGAAATAGA‑TTGTTTGACTTTAAAAAAAAATAAATTGAAAAAAAAGATAAAAAAAAAGCCAGCGGGGGCTGGGTCTTGTAAAAGCCAAAATAGAAGCTGGCggt                                                                          >  1:497127/1‑147 (MQ=255)                                                                                tGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTGCAAATAGA‑TTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTAc                                                                        <  2:499309/150‑1 (MQ=255)                                                                                 gCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTGCAAATAGA‑TTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTAcg                                                                       <  1:156948/150‑1 (MQ=255)                                                                                 gCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGGTGCGAAAAAA‑TTGGTTTGATTAAAAAAAAAAAAAATTGACAGAAAAAAAAAAAAAAAAAACAGCGGGCGCGGGGCCTTGAAAAAGCTAAAATAAAAAATGGCGGTAcgc                                                                      >  2:134847/1‑151 (MQ=255)                                                                                         atatTCCGTAACAGGATGATCGTTATGGC‑GGGGGTGCAAAAACA‑TTTCTTTTTTTTAAAAAAAAATAAATTTATACAAAAAAAAAAAAAAAAAACAACGGGGGCCGGCTCTTTAAGAAGGTAAAATAAAAAATGGGGGTTCGCGGAgg                                                                 >  1:45728/1‑147 (MQ=255)                                                                                                   aCAGGATGATCGTTATGGC‑GGGGTTGCAAATAGA‑TTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGa                                                    <  2:460989/151‑1 (MQ=255)                                                                                                    cAGGATGATCGTTATGGC‑GGGGTTGCAAATAGA‑TTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGaa                                                   <  2:634450/151‑1 (MQ=255)                                                                                                                         ggTTGCAAATAGA‑TTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGc                               >  1:135327/1‑151 (MQ=255)                                                                                                                          gTTGCAAATAGA‑TTGCTTGACTTAACAAACAGATAACTTGAAAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCa                              <  1:61635/151‑1 (MQ=255)                                                                                                                            tGCAAATAGA‑TTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCAc                             <  1:580338/150‑1 (MQ=255)                                                                                                                             gCAAATAGA‑TTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCACGc                           >  1:35262/1‑151 (MQ=255)                                                                                                                                  tAGA‑TTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGTGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGCAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCACGCCAg                        >  2:100777/1‑149 (MQ=255)                                                                                                                                     a‑TTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCACGCCAGTTACg                   <  2:241204/151‑1 (MQ=255)                                                                                                                                       ttGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCACGCCAGTTACGt                  >  2:232809/1‑151 (MQ=255)                                                                                                                                            tGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCACGCCAGTTACGTAAGc              <  2:827106/150‑1 (MQ=255)                                                                                                                                               cTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCACGCCAGTTACGTAAGCAAt           >  1:653717/1‑150 (MQ=255)                                                                                                                                                   acaaacaGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCACGCCAGTTACGTAAGCAATCAGAc      >  2:810656/1‑151 (MQ=255)                                                                                                                                                    caaacaGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCACGCCAGTTACGTAAGCAATCAGACg     <  2:456618/151‑1 (MQ=255)                                                                                                                                                       acaGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCACGCCAGTTACGTAAGCAATCAGACGTTc  >  2:643052/1‑151 (MQ=255)                                                                                                                                                        |                                                                                                                                                      ATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGC‑GGGGTTGCAAATAGA‑TTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCACGCCAGTTACGTAAGCAATCAGACGTTC  >  NC_000913/987373‑987671

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑