Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,578,143	0	A	C	47.8%	62.6 / 11.4	46	L79V (TTA→GTA)	maeB	malic enzyme: putative oxidoreductase/phosphotransacetylase
Reads supporting (aligned to +/- strand):  ref base A (21/3);  new base C (0/22);  total (21/25)
Fisher's exact test for biased strand distribution p-value = 2.95e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGAGCGCGGCGACAACTTCAATAAATTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCT‑TAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAATGTT‑GCC‑TAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGCCAGCGCCAGATCGCG  >  NC_000913/2577999‑2578281                                                                                                                                                    |                                                                                                                                           cGAGCGCGGCGACAACTTCAATAAATTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCT‑TAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAATGTC‑GCC‑TAAcccc                                                                                                                                        >  2:653261/1‑149 (MQ=255)            aCAACTTCAATAAATTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCT‑TAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAATGTT‑GCC‑TAACCCCAGCACCGCCGTAc                                                                                                                           >  1:808645/1‑151 (MQ=255)                 ttCAATAAATTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCT‑TAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAATGTT‑GCC‑TAACCCCAGCACCGCCGTACCGtt                                                                                                                       >  2:90339/1‑150 (MQ=255)                  tCAATAAATTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCT‑TAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAATGTT‑GCC‑TAACCCCAGCACCGCCGTACCGtt                                                                                                                       >  2:386973/1‑149 (MQ=255)                    aataatTTTGTCCGGGTCGAGTTCGTCAACTTAAATTTAAAATACACCAACCCCGGCAAATTTCT‑AAAACAAAACGCCCTTGCCTCCCATCCCCGGTTTGCCTGCCAGCGCGCAATTTTT‑CCC‑AACCCCCAGCACCGCCGTACCGTTag                                                                                                                     <  1:445695/149‑1 (MQ=255)                     aTAAATTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCT‑TAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAATGTT‑GCC‑TAACCCCAGCACCGCCGTACCGTTag                                                                                                                     >  1:392303/1‑148 (MQ=255)                         aTTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCT‑TAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAATGTT‑GCC‑TAACCCCAGCACCGCCGTACCGTTAGAGATCAc                                                                                                              >  1:443611/1‑151 (MQ=255)                              tCCGGGTCGAGTTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCT‑TAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAATGTT‑GCC‑TAACCCCAGCACCGCCGTACCGTTAGAGATCACCGcc                                                                                                          >  1:497202/1‑150 (MQ=255)                               ccGGGTCGAGTTCGTAAACTTCATTTAAAAATACACCAACCCCGGCAAATTTCT‑AAAACAGACCCCCCTTGCCTCCCACCCCCGGTTTGCCTGCCAGCGCCCAAATGTT‑CCC‑TAACCCCAGCCCCGCCGTACCGTTAGAGATCACCGcca                                                                                                         <  1:122758/150‑1 (MQ=255)                                      gatttCGTCAACTTCAATGTCAAATACATCAACCCCGGCAATTTTTT‑AAAACAGAACCCCCTTGCCTCCCATCCCCGGTTTGCCTGCCAGCCCCCCAATGTC‑CCC‑AACCCCCAGCCCCGCCGTACCGTTAGAGATCACCGCCACCAGGTTa                                                                                                 <  2:151640/148‑1 (MQ=255)                                          tCGTAACCTTCATTGTCAAATACACCAACCCCGGCGATTTTCT‑TAAACAGACCCCCCTTCCCTCCCACCCCCGTTTTGCCTGCCAGCGCCCAATTGTT‑GCC‑TACCCCCACCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCt                                                                                              <  2:837638/150‑1 (MQ=255)                                           cGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCT‑TAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAATGTT‑GCC‑TAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCg                                                                                            >  2:804457/1‑151 (MQ=255)                                               aaCTTAAATGTAAAATACATCAACCCCGGCGATTTTCT‑AAAACAGAACCCCCTTGCCTCCCACCCCCGTTTGCCCTGCCAGCGCGCAAATTTT‑GCC‑AACCCCCACCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGc                                                                                         <  1:838101/150‑1 (MQ=255)                                                    cAATGTCAAATACATCAATCCCGGCGAATTTCT‑TAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAATGTT‑GCC‑TAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGtat                                                                                    >  2:752647/1‑150 (MQ=255)                                                     aaTTTCAAAACCACCAACCCCGGCAAATTTCT‑AAAACAGAACGCCCTTGCCTCCCATCACCGGTTTGCCTCCCAGCGCGCCATTGTT‑GCA‑TACCCCCAGCCCCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTatat                                                                                  <  2:82211/151‑1 (MQ=255)                                                     aaTGACAAACACATCAACCCCGGCAATTTCCT‑AAAACAGACCGCCCTTGCCTCCCATCCCCGTTTCCCCGCCCAGCGCCCAAATTTT‑CCC‑TACCCCAAGCCCCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGtat                                                                                    <  2:294480/149‑1 (MQ=255)                                                      aTGTCAAATACATCAATCCCGGCGAATTTCT‑TAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAATGTT‑GCC‑TAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATAtt                                                                                 >  2:708271/1‑151 (MQ=255)                                                           aaaTACATCAATCCCGGCGAATTTCT‑TAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAATGTT‑GCC‑TAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGAATATTTGt                                                                              >  2:352895/1‑149 (MQ=255)                                                               aCATCAACCCCGGCGATTTTCT‑AAAACAGACCCCCTTTGCTTCCCATCCCCGTTTTGCCTCCCGGCGCGCAAATGTT‑CCT‑TACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCt                                                                         <  1:562050/150‑1 (MQ=255)                                                                cATCAATCCCGGCGAATTTCT‑TAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAATGTT‑GCC‑TAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCtt                                                                        >  1:174277/1‑150 (MQ=255)                                                                    accccgggCGATTTTTT‑AAAACAGACCGCCCTTCCCTCCCATCCCCGTTTTGCCTCCCAGC‑CGGCAATTTTGGCC‑TACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGc                                                                          <  1:507104/138‑1 (MQ=255)                                                                    aacccgggCGATTTTCT‑AAAACAGACCGCCCTTGCCTCCCACCACCGGTTTGCCTCCCAGCGCGCCAATGTT‑GCC‑TACCCCCGGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCttt                                                                       <  1:212823/141‑1 (MQ=255)                                                                    aaccccGGCGATTTTCT‑TAAACAGACCCCCCTTGCCTTCCACCCCCGGTTTGCCTGCCAGCGCCCCAATGTT‑GCC‑AACCCCCAGCCCCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAAc                                                                   <  1:976054/148‑1 (MQ=255)                                                                      ccccGGCGAATTTCT‑AAAACAGACCGCCCTTGCCTCCCACCCCCGGTTTGCCTGCCGGCGCGCAAATGTT‑GCC‑AACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACgg                                                                 <  1:152696/150‑1 (MQ=255)                                                                      ccccGGC‑AATTTCTGTAAACAGCGCCCCCTTCCTTCCCCCCCCCGCTTTGCCTCCCGGCCCCCCAATGTC‑CCC‑TAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCGCCAGGTTACCTCGGGCGGTATATTTGTAGGCt                                                                         <  2:838626/142‑1 (MQ=255)                                                                              attttCT‑AAAACAGACCCCCCTTCCCTCCCACCCCCGTTTTCCCTGCCAGCGCCCAATTGTT‑GCC‑TACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCttttt                                                         <  1:652957/149‑1 (MQ=255)                                                                               aTTTCT‑TAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAATGTT‑GCC‑TAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTc                                                        >  2:713438/1‑151 (MQ=255)                                                                                tttCT‑AAAACAAACCCCCCTTCCCTCCCACCCCCGTTTTGCCTGCCAGCGCGCAAATGTT‑CCC‑TACCCCCAGCCCCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTc                                                        <  1:202322/150‑1 (MQ=255)                                                                                 ttCT‑TAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAATGTT‑GCC‑TAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCg                                                       >  1:145218/1‑150 (MQ=255)                                                                                  tCT‑TAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAATGTT‑GCC‑TAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGAt                                                     >  1:724371/1‑151 (MQ=255)                                                                                          cAGAACGCCTTTGCCTCCCACCACCTGTTTGCCGGCAAGCGGGCAAATGTT‑GCC‑TAACCCAAGAACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCa                                                 <  1:185490/148‑1 (MQ=255)                                                                                           agaccccccttcccttCCACCCCCGGTTTGCCTGCCAGCGCCCAAATGTT‑GCC‑TACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAg                                               <  1:219595/143‑1 (MQ=255)                                                                                               cGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAATGTT‑GCC‑TAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAgg                                         >  1:538136/1‑151 (MQ=255)                                                                                                 cccttcccttCCACCCCCGTTTTGCCTGCCAGCCCCCAAATGTT‑CCC‑TACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGt                                        <  2:272049/150‑1 (MQ=255)                                                                                                  ccTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAATGTT‑GCC‑TAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGc                                      >  2:654094/1‑151 (MQ=255)                                                                                                     tGCCTCCCATCCCCGGTTTGCCTCCCAGCGCGCCAATTTT‑CCC‑TACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCg                                     <  1:622761/149‑1 (MQ=255)                                                                                                               ccccGGTTTCCTTGCCGGCGC‑CCAAATTT‑GCCTTACCCCCAGCCCCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGt                         <  1:603228/149‑1 (MQ=255)                                                                                                               ccccGGTTTCCCTGCCGGCGCGCAAATGTT‑CCC‑TACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCt                            <  1:304353/146‑1 (MQ=255)                                                                                                                   gttttCCCTGCCAGCGCCCCATTGTT‑CCC‑TACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAg                      <  2:754261/148‑1 (MQ=255)                                                                                                                        gcctgccAGCGCGCCAATGTT‑GCC‑TAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGcc                >  1:576088/1‑151 (MQ=255)                                                                                                                             ccggccccccATTGTT‑GCC‑TACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGCCAgc             <  1:355672/141‑1 (MQ=255)                                                                                                                             ccAGCGCGCCATTGTT‑GCC‑CACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGCCAgcgc           <  1:395429/151‑1 (MQ=255)                                                                                                                                gcgcgcCAATGTT‑GCC‑TAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGCCAGCGcc          >  1:161000/1‑149 (MQ=255)                                                                                                                                   ccccAAGGTT‑GCC‑CACCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGCCAgcg            <  1:558860/142‑1 (MQ=255)                                                                                                                                     ccAATGTT‑GCC‑TAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGCCAGCGCCAGATcgc   >  1:489997/1‑151 (MQ=255)                                                                                                                                      cAATGTT‑GCC‑TAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGCCAGCGCCAGATcgcg  >  1:640247/1‑151 (MQ=255)                                                                                                                                                    |                                                                                                                                           CGAGCGCGGCGACAACTTCAATAAATTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAATACATCAATCCCGGCGAATTTCT‑TAAACAGAACGCCCTTGCCTTCCATCACCGGTTTGCCTGCCAGCGCGCCAATGTT‑GCC‑TAACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGCCAGCGCCAGATCGCG  >  NC_000913/2577999‑2578281

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑