Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,443,277	0	A	C	44.0%	72.3 / 18.6	50	V274G (GTA→GGA)	secY	preprotein translocase membrane subunit
Reads supporting (aligned to +/- strand):  ref base A (25/3);  new base C (0/22);  total (25/25)
Fisher's exact test for biased strand distribution p-value = 5.18e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACGCATAGAGTAACACATAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAAATACTAATACT  >  NC_000913/3443131‑3443426                                                                                                                                                   |                                                                                                                                                      aCGCATAGAGTAACACATAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTAcccc                                                                                                                                                   >  1:983973/1‑151 (MQ=255)  cGCATAGAGTAACACATAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTAccccc                                                                                                                                                  <  2:943784/151‑1 (MQ=255)       agagTAACCCATAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCAGTCCCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCa                                                                                                                                              <  2:759353/150‑1 (MQ=255)          gTAACACATAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATAtt                                                                                                                                          >  1:774515/1‑151 (MQ=255)             acacATAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGTGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCAc                                                                                                                                       >  2:244417/1‑151 (MQ=255)              cacaTAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACt                                                                                                                                      >  2:867010/1‑151 (MQ=255)                       cGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCgg                                                                                                                              >  2:418638/1‑150 (MQ=255)                       cGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGt                                                                                                                             >  1:348721/1‑151 (MQ=255)                        ggtgccccgggcgccAAATACAGCGAATTTGTTGCCAGCCAGTCCCACCCAGTCCCCCCCCCAAACAATGACGCGATGGTCGCCGGAAACAAAATAATACGGGAAGGGAAGTTTGCCGGAATTCCCCCCGCCATATTCACTTTCAGAGGt                                                                                                                             <  2:705184/136‑1 (MQ=255)                           tGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAAt                                                                                                                         >  1:449004/1‑151 (MQ=255)                             cccAGGCAGAAAAAACAGAAAATTTTTTTCCAGCCATTCCCACCCAGCCCCCCCCCCAACCCATGACGCGAGGGCCGCCGGAAACAAAATAATACGGGAGGGAAAATTTGCGGGGATCCCCCCCGCCATATTCACTTTCAGCGGTAAAtg                                                                                                                        <  2:694746/150‑1 (MQ=255)                                 ggCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGc                                                                                                                   >  1:383386/1‑151 (MQ=255)                                 ggCTGAAAATACAGCAAATTTTTTGCCAGCCATTCCCACCCAGTCCCCCCCCCGACCCAGGACGCGATGGTCGCCGGAAACAAAATAATACTGGAAGCGAAGATTGCCGGGATTCCCCCCGCCATATTCACTTTCAGCGGTAAAtgtg                                                                                                                      <  1:705374/148‑1 (MQ=255)                                    tGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGctct                                                                                                                >  2:790437/1‑151 (MQ=255)                                              gcaaatttgttgTCAGCCATTCCCAACCAGCCCCCCCCCCGACCCATGACGCGTGGGTCGCGGGGAACAAAATAATACGGGAGGCGAAGATTGCGGGGATTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCAt                                                                                                       <  2:969327/144‑1 (MQ=255)                                               aaaaaTTTTTGTTCGCACGTCCCACCCATCACCCCCCCCCACCCATGACGCGTTGGTCGCCGGAAAAACAATATCTTGGGAAGGAAAATTTGCCGGTATTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATa                                                                                                      <  1:676676/148‑1 (MQ=255)                                                gAAATTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCAt                                                                                                       >  1:766577/1‑148 (MQ=255)                                                       ttgcCACCCATTCCCACCCAGTCCCCCCCCCAAACCATGCCGCGATGGCCGCCGGAAACAAAATAATCCGGGAGGCGAAGATGGCCGGGTTTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACacgac                                                                                              <  1:601983/150‑1 (MQ=255)                                                             gcctgtccaaaCAAGTCCCGCCCCGCAACCAGGACGGAATGGACGGCGGGAACAAAATAATGCTGGAAGCGAAAATTGCGGGGATAACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCtt                                                                                        <  1:738022/141‑1 (MQ=255)                                                             gCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTg                                                                                       >  1:975836/1‑151 (MQ=255)                                                              ccAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGc                                                                                      >  2:90873/1‑151 (MQ=255)                                                                   tCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACg                                                                                 >  2:405919/1‑151 (MQ=255)                                                                      acccAGTCCCCCCCCGAAACCATGCCGCGGTGGTCGCGGGAAACAAAATATTAGTGGAAGCGAAGTTTGCGGGTTTTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGtt                                                                               <  2:3218/148‑1 (MQ=255)                                                                      aaCCAGTACCGCCTCCGAACCATGGCGCGATGGTCGCCGGGAAAAGACTACTACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTAACTTTCAGCGGTAAATGTGTGCGCTGTGCAGCATAGACACGACGACCTTGCTGACGttt                                                                              >  2:962869/1‑151 (MQ=255)                                                                      aaCCAGCCCCCCCCCCGAACCATGCCGCGATGGTCGCCGGAAACAAAATAATACTGGAAGCGAAGTTTGCCGGGATTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCt                                                                                     <  1:101896/144‑1 (MQ=255)                                                                        ccattcccccccccGAACCATGACGGGTTGGTCGCGGGAAAAAAAAAAATACGGGAAGCGAAGTTGGCGGGGATTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTc                                                                             <  1:3539/141‑1 (MQ=255)                                                                        ccAGTCCCCCCCCCAAACCAGGAGGCGATGGTCGCCGGGAAAAAAAAAATACGGGAAGAAAAGATGGCGGGGATTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTcg                                                                            <  1:331585/151‑1 (MQ=255)                                                                         cAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGACATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTcgc                                                                           >  2:323769/1‑151 (MQ=255)                                                                           gtcccGCCCCCAAACCAGGACGGGAGGGTCGCGGGAAACAAAATAATACTGAAAGAAAAGAGTGCGGGGATTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTcg                                                                            <  1:879088/145‑1 (MQ=255)                                                                              ccccccccGACCCATGACGAGAGGGCCGCCGGAAAAAAAATAATACTGGAAGCGAAGATTGCCGGGATTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTcgcg                                                                          <  2:374643/144‑1 (MQ=255)                                                                                gCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGttt                                                                    >  2:976549/1‑151 (MQ=255)                                                                                  ccccAAACCAGGCCGCATTGGTCGCGGAAAACATAATAATACGGAAAGCGAAGTTTGCGGGGATTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTAc                                                                  <  1:615292/151‑1 (MQ=255)                                                                                       aaCCAAGACGGGGTGTTCCCGGGAAAAAAAATAATTCTGAACGGGAAGTTCGTCGTGTTCCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACcac                                                               <  2:130715/149‑1 (MQ=255)                                                                                                 cgATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCACGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTg                                                   >  2:424301/1‑151 (MQ=255)                                                                                                         gCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCt                                           >  2:112948/1‑151 (MQ=255)                                                                                                            ggaaaaaaaataatACGGGAAGGGAAGATGGCGGGAATTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCt                                           <  2:472400/140‑1 (MQ=255)                                                                                                               aaCAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTcaaca                                      >  1:499403/1‑150 (MQ=255)                                                                                                               aaCAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTcaaca                                      >  1:612357/1‑150 (MQ=255)                                                                                                                 cAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAAt                                   >  1:708835/1‑151 (MQ=255)                                                                                                                       aatgCTGGAAGCAAAGGTGGCGGAGTTGCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATacaac                              <  2:118788/150‑1 (MQ=255)                                                                                                                                  cGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCAc                  >  1:770143/1‑151 (MQ=255)                                                                                                                                    aaGATTGCGGGGATTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTc                    <  1:188119/147‑1 (MQ=255)                                                                                                                                    aaGATTGCGGGGATTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTg                <  1:244442/151‑1 (MQ=255)                                                                                                                                     aGATTGCCGGATTCCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACt                 <  2:176480/149‑1 (MQ=255)                                                                                                                                          gcggggATTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAaat           <  1:418686/147‑1 (MQ=255)                                                                                                                                             gggATTCCCCCCGCCATATTCACTTTTAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCaaa            <  2:369772/146‑1 (MQ=255)                                                                                                                                             gggATCCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAaatacta       <  2:202897/151‑1 (MQ=255)                                                                                                                                               gATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAaatactaat     >  2:497776/1‑151 (MQ=255)                                                                                                                                                 ttACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAaatactaatac   >  2:389127/1‑151 (MQ=255)                                                                                                                                                  tACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAaatactaatact  >  2:226396/1‑151 (MQ=255)                                                                                                                                                   |                                                                                                                                                      ACGCATAGAGTAACACATAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAAATACTAATACT  >  NC_000913/3443131‑3443426

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑