Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,019,592	0	A	T	35.7%	46.5 / 11.0	28	L144F (TTA→TTT)	ssnA	putative chlorohydrolase/aminohydrolase
Reads supporting (aligned to +/- strand):  ref base A (2/16);  new base T (10/0);  total (12/16)
Fisher's exact test for biased strand distribution p-value = 5.03e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCCCTTGATGAAGAGTCGCTCTATTACAGCGGACTGATTTGTTCCCTGGAAGCGATTAAGAGCGGATGTACATCGGTTATCGATCACCATGCCTCTCCGGCGTATATCGGCGGGTCGCTCTCCACATTGCG‑CGACGCATTTTTAAAAGTTGGCCTGCGCGCGATGACCTGTTTTGAAACTACTGACCGTAACAACGGCATCAAAGAGTTGCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCCGTATCTGGTG  >  NC_000913/3019449‑3019739                                                                                                                                                 |                                                                                                                                                    gcCCTTGATGAAGAGTCGCTCTATTACAGCGGACTGATTTGTTCCCTGGAAGCGATTAAGAGCGGATGTACATCGGTTATCGATCGCCATGCCTCTCCGGCGTATATCGGCGGGTCGCTCTCCACATTGCG‑CGACGCATTTTTAAAAGTTg                                                                                                                                              <  2:321385/151‑1 (MQ=255)  cccTTGATGAAGAGTCGCTCTATTACAGCGGACTGATTTGTTCCCTGGAAGCGATTAAGAGCGGATGTACATCGGTTATCGATCACCATGCCTCTCCGGCGTATATCGGCGGGTCGCTCTCCACATTGCG‑CGACGCATTTTTAAAAGTTgg                                                                                                                                             <  2:296311/151‑1 (MQ=255)   ccTTGATGAAGAGTCGCTCTATTACAGCGGACTGATTTGTTCCCTGGAAGCGATTAAGAGCGGATGTACATCGGTTATCGATCACCATGCCTCTCCGGCGTATATCGGCGGGTCGCTCTCCACATTGCG‑CGACGCATTTTTAAAAGTTGGc                                                                                                                                            <  1:210869/151‑1 (MQ=255)          gaAGAGTCGCTCTATTACAGCGGACTGATTTGTTCCCTGGAAGCGATTAAGAGCGGATGTACATCGGTTATCGATCACCATGCCTCTCCGGCGTATATCGGCGGGTCGCTCTCCACATTGCG‑CGACGCATTTTTAAAAGTTGGCCTgcga                                                                                                                                      <  1:294014/150‑2 (MQ=255)                    tctATTACAGCGGACTGATTTGTTCCCTGGAAGCGATTAAGAGCGGATGTACATCGGTTATCGATCACCATGCCTCTCCGGCGTATATCGGCGGGTCGCTCTCCCCCCTTCG‑CGCCGCATTTTTTTAAATTGGGCTGCGCGCGATGAcc                                                                                                                             >  2:282969/1‑149 (MQ=255)                      tATTACAGCGGACTGATTTGTTCCCTGGAAGCGATTAAGAGCGGATGTACATCGGTTATCGATCACCATGCCTCTCCGGCGTATATCGGCGGGTCGCTCTCCACAATGCG‑CGACGCCTTTTTTAAAATTGGGCTGCGCGCGGTGACCTGtt                                                                                                                         >  2:169629/1‑151 (MQ=255)                      tATTACAGCGGACTGATTTGTTCCCTGGAAGCGATTAAGAGCGGATGTACATCGGTTATCGATCACCATGCCTCTCCGGCGTATATCGGCGGGGGGCTCTTCCCCCTGCG‑CGTCGCGTTTTTTTAAGTTGGACCGGGCGCGGTGACCTGtt                                                                                                                         >  2:70374/1‑151 (MQ=255)                       aTTACAGCGGACTGATTTGTTCCCTGGAAGCGATTAAGAGCGGATGTACATCGGTTATCGATCACCATGCCTCTCCGGCGTATATCGGCGGGTCGCTCTCCACATTGCG‑CGACGCATTTTTAAAAGTTGGCCTGCGCGCGATGACCTGtt                                                                                                                         <  1:87482/150‑1 (MQ=255)                           cAGCGGACTGATTTGTTCCCTGGAAGCGATTAAGAGCGGATGTACATCGGTTATCGATCACCATGCCTCTCCGGCGTATATCGGCGGGTTGCCCCCCCCATTGCT‑CGGCGCCTTTTTTAAAATTGGGCTGGGCGCGCTGACCtccttt                                                                                                                       >  1:298936/1‑143 (MQ=255)                                gACTGATTTGTTCCCTGGAAGCGATTAAGAGCGGATGTACATCGGTTATCGATCACCATGCCTCTCCGGCGTATATCGGCGGGGCGGCCTCCACCCTGCC‑GGGCGCCTTTTTTAAAGATTGCCTGCGCGCGAGGACCCGTGTTGtaa                                                                                                                   >  1:388376/1‑147 (MQ=255)                                        tGTTCCCTGGAAGCGATTAAGAGCGGATGTACATCGGTTATCGATCACCATGCCTCTCCGGCGTATATCGGCGGGTCGCGCTTCACATTGGG‑CGGCGCCCTTTTTTAAATTGGCCGGCGCCCGCTGACCTCCTTTGtaa                                                                                                                   >  1:291296/1‑139 (MQ=255)                                             ccTGGAAGCGATTAAGAGCGGATGTACATCGGTTATCGATCACCATGCCTCTCCGGCGTATATCGGCGGGTCGCTCTCCACATTGCG‑CGACGCATTTTTAAAAGTTGGCCTGCGCGCGATGACCTGTTTTGAAACTACTGACCGTaacaac                                                                                                  <  2:169331/151‑1 (MQ=255)                                                ggAAGCGATTAAGAGCGGATGTACATCGGTTATCGATCACCATGCCTCTCCGGCGTATATCGGCGGGTCGCTCTCCACATTGCG‑CGACGCATTTTTAAAAGTTGGCCTGCGCGCGATGACCTGTTTTGAAACTACTGACCGTAACAACgg                                                                                                <  1:40911/150‑1 (MQ=255)                                                ggAAGCGATTAAGAGCGGATGTACATCGGTTATCGATCACCATGCCTCTCCGGCGTATATCGGCGGGTCGCTCTCCACATTGCG‑CGACGCATTTTTAAAAGTTGGCCTGCGCGCGATGACCTGTTTTGAAACTACTGACCGTAACAACGGc                                                                                               <  2:285454/151‑1 (MQ=255)                                                      gATTAAGAGCGGATGTACATCGGTTATCGATCACCATGCCTCTCCGGCGTATATCGGCGGGTCGCTCTCCACATTGCG‑CGACGCATTTTTAAAAGTTGGCCTGCGCGCGATGACCTGTTTTGAAACTACTGACCGTAACAACGGCATCaaa                                                                                         <  1:153275/151‑1 (MQ=255)                                                      gATTAAGAGCGGATGTACATCGGTTATCGATCACCATGCCTCTCCGGCGTATATCGGCGGGTCGCTCTCCACATTGCG‑CGACGCATTTTTAAAAGTTGGCCTGCGCGCGATGACCTGTTTTGAAACTACTGACCGTAACAACGGCATCaaa                                                                                         <  2:212623/151‑1 (MQ=255)                                                                ggATGTACATCGGTTATCGATCACCATGCCTCTCCGGCGTATATCGGCGGGGCGCTCTCCCCATTTCGCCGCCCCTTTTTTTAAAATTGG‑CTGCCCGCGAGGACCTGTTTTTTAAATACTGACCGGAAAAAACGCATCAAAAAGGTGGAg                                                                                >  2:341368/1‑150 (MQ=255)                                                                     tACATCGGTTATCGATCACCATGCCTCTCCGGCGTATATCGGCGGGTCGCTCTCCACATTTCG‑CGACGCCTTTTTTAAAGTTTGCCTGCGCGCGGTGACCTGTTTTTTTAATACTTACCGTAACAACAGCATCAAAGAGATGGAgg                                                                               >  2:45090/1‑146 (MQ=255)                                                                                 cGATCACCATGCCTCTCCGGCGTATATCGGCGGGTCGCCCTCCCCATTGTG‑CGGCGCACTTTTTTAAAATGGGCTGCGCGCGGTGAACTGTTTTTTAAATACTGACCCCCAAAACCGCCTCCAAAAGGTGCGGGGAGGGGGAGAAGaaaa                                                               >  2:119089/1‑150 (MQ=255)                                                                                    tCACCATGCCTCTCCGGCGTATATCGGCGGGTCGCTCTCCCCACTTCG‑CGACGCCTTTTTTAAAAATGGGCTGCGCGCGGTGACCCGTTTTTTAAATACTTACCGTAACAACCGCATCAAAGAGGTGCAGGGAGGGGGAGAAGaaaaaaa                                                            >  2:359005/1‑147 (MQ=255)                                                                                     cACCATGCCTCTCCGGCGTATATCGGCGGGTCGCTCTCCACATTGCG‑CGACGCATTTTTAAAAGTTGGCCTGCGCGCGATGACCTGTTTTGAAACTACTGACCGTAACAACGGCATCAAAGAGTTGCAGGAAGGTGTAGAAGAAAACATcc                                                          <  2:20807/151‑1 (MQ=255)                                                                                       ccATGCCTCTCCGGCGTATATCGGCGGGTCGCTCTCCACATTGCG‑CGACGCATTTTTAAAAGTTGGCCTGCGCGCGATGACCTGTTTTGAAACTACTGACCGTAACAACGGCATCAAAGAGTTGCAGGAAGGTGTAGAAGAAAACATCCGt                                                        <  2:44179/151‑1 (MQ=255)                                                                                         aTGCCTCTCCGGCGTATATCGGCGGGTCGCTCTCCACATTGCG‑CGACGCATTTTTAAAAGTTGGCCTGCGCGCGATGACCTGTTTTGAAACTACTGACCGTAACAACGGCATCAAAGAGTTGCAGGAAGGTGTAGAAGAAAACATCCGttt                                                      <  2:330554/151‑1 (MQ=255)                                                                                                          atCGGCGGGTCGCTCTCCACATTGCG‑CGACGCATTTTTAAAAGTTGGCCTGCGCGCGATGACCTGTTTTGAAACTACTGACCGTAACAACGGCATCAAAGAGTTGCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGATtgatg                                     <  2:360874/151‑1 (MQ=255)                                                                                                                     gCTCTCCACATTGCG‑CGACGCATTTTTAAAAGTTGGCCTGCGCGCGATGACCTGTTTTGAAACTACTGACCGTAACAACGGCATCAAAGAGTTGCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCgaagaa                           >  2:118107/1‑150 (MQ=255)                                                                                                                            acaTTGCG‑CGACGCATTTTTAAAAGTTGGCCTGCGCGCGATGACCTGTTTTGAAACTACTGACCGTAACAACGGCATCAAAGAGTTGCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACa                    >  2:134219/1‑150 (MQ=255)                                                                                                                                       aCGCATTTTTAAAAGTTGGCCTGCGCGCGATGACCTGTTTTGAAACTACTGACCGTAACAACGGCATCAAAGAGTTGCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCCGTa         <  2:299054/151‑1 (MQ=255)                                                                                                                                               ttAAAAGTTGGCCTGCGCGCGATGACCTGTTTTGAAACTACTGACCGTAACAACGGCATCAAAGAGTTGCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCCGTATCtggtg  <  2:138291/150‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                    GCCCTTGATGAAGAGTCGCTCTATTACAGCGGACTGATTTGTTCCCTGGAAGCGATTAAGAGCGGATGTACATCGGTTATCGATCACCATGCCTCTCCGGCGTATATCGGCGGGTCGCTCTCCACATTGCG‑CGACGCATTTTTAAAAGTTGGCCTGCGCGCGATGACCTGTTTTGAAACTACTGACCGTAACAACGGCATCAAAGAGTTGCAGGAAGGTGTAGAAGAAAACATCCGTTTCGCCCGTTTGATTGATGAGGCGAAGAAAGCGACAAGCGAGCCGTATCTGGTG  >  NC_000913/3019449‑3019739

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑