Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,840,646	0	T	C	41.9%	59.8 / 10.9	43	D365G (GAT→GGT)	nepI	putative transporter
Reads supporting (aligned to +/- strand):  ref base T (18/7);  new base C (0/18);  total (18/25)
Fisher's exact test for biased strand distribution p-value = 8.66e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGATATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGAC‑AACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGACCAGCCGACGGGAACCAATGCAAA  >  NC_000913/3840497‑3840785                                                                                                                                                       |                                                                                                                                            ccGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGATATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGAC‑AACATCAACGGCGAAGTCAGACCAATATTATc                                                                                                                                            <  2:342316/151‑1 (MQ=255)    gATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGATATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGAC‑AACATCAACGGCGAAGTCAGACCAATATTATCCAg                                                                                                                                         <  2:228753/151‑1 (MQ=255)       atGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGATATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGAC‑AACATCAACGGCGAAGTCAGACCAATATTATCCAgcgc                                                                                                                                      >  1:527621/1‑151 (MQ=255)       atGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGATATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGAC‑AACATCAACGGCGAAGTCAGACCAATATTATCCAgcg                                                                                                                                       <  2:719473/150‑1 (MQ=255)            aGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGATATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGAC‑AACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAAc                                                                                                                                 >  1:632852/1‑151 (MQ=255)              aaCAGCAACAACTACTGACCAACGCTTCTTTACCTGATATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGAC‑AACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAAccg                                                                                                                               <  1:693940/151‑1 (MQ=255)                                  aaCGCTTCTTTCCCTGATATCAGTTTTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGAC‑AACATCACCGGCGAAGTCAGACCAATATTACCCAGCGCAAAACCGCCGATTGCCGCGCCACAGGt                                                                                                           <  2:62864/151‑1 (MQ=255)                                  aaCGCTTCTTTACCTGATATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGAC‑AACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGt                                                                                                           >  2:531025/1‑151 (MQ=255)                                   aCGCTTCTTTCCCTAATATCAGGTTTTCTTCATTTTCCCCTTTGCAGTAACCAACAATGCAGTCAGCACCATCAATGGGCCGGAC‑AACATCACCGGCGAGGTCAAACCAATATTACCCAGCGAATAACCGCCGATTGCCGCGCCACAgg                                                                                                            <  2:425225/149‑1 (MQ=255)                                       ttttttACCTGATAAAAGGATTTCTTCATTTCCCCCTTTGAAGCACCCAACAATGCAGCCAGCACCTTCAATGTGCCGCAA‑AACAACACCGGCGAAGTAAGCCCAATTTTACCCAGCCCATAACCGCCGATTGCCGCGCcaca                                                                                                              <  2:327241/140‑1 (MQ=255)                                        tcttTACCTGATATCAGGATTTCTTCATTTCCCCCTTTGCAGAAACAAACAATGCATTCAGCAAAATCAATGTGCCGAAC‑AAAACAAACGGCGAAGACAGACCAATATTATCCAGCGCAAAACCGCCGATTGCCGCGCCACAGGTATTAg                                                                                                      <  1:4814/150‑1 (MQ=255)                                           ttACCTGATATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGAC‑AACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCa                                                                                                    >  2:236435/1‑149 (MQ=255)                                              ccTGATATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGAC‑AACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACCGGTATTAGCAAGCTg                                                                                               >  2:76419/1‑151 (MQ=255)                                                    atCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGAC‑AACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATaa                                                                                          >  2:538206/1‑150 (MQ=255)                                                                 cATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGAC‑AACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAAt                                                                             >  1:610521/1‑150 (MQ=255)                                                                    ttcccccTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGAA‑AACATCAACGGCGAAGTCAGACCAATATTATCCAGCGAAAAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGa                                                                          <  2:26943/145‑1 (MQ=255)                                                                    ttcccccTTTGAAGAAACCAACAACGCGGCCAAAAACATCAATTTG‑CGGACAAACTCCAACGGCGAATACACACAAATATTACCCAGCGAATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAg                                                                           <  1:536723/144‑1 (MQ=255)                                                                       cACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGAC‑AACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCg                                                                      >  1:406540/1‑151 (MQ=255)                                                                         ccTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGAC‑AACATCAACGGCGAAGCCAGACCAATATTACCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCgg                                                                     <  2:265530/150‑1 (MQ=255)                                                                                agaaacaaacaATGCAGTCACAAACATCAATGTGCCGAAC‑AACACCACCGGCGAAGTCAGACCAATATTATCCACCCCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCt                                                             <  2:328638/148‑1 (MQ=255)                                                                                aGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGAC‑AACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCt                                                             >  2:378060/1‑151 (MQ=255)                                                                                aGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGAC‑AACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCt                                                             >  2:130938/1‑151 (MQ=255)                                                                                 gTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGAC‑AACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTg                                                            >  2:787448/1‑151 (MQ=255)                                                                                 gTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGAC‑AACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTg                                                            >  1:70241/1‑151 (MQ=255)                                                                                   aacaaacaATGCAGTCAGCAACATAAATGTGCCGAAC‑ACCACCAACGGCGAAGTCAGCCAAATATTACCCAGCACATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTg                                                            <  2:547632/149‑1 (MQ=255)                                                                                   aacaaacaATGCAGCAAACAACATAAATGTGCCGGAC‑AACATCACCGGCGAAGTCAGACCAATATTACCCAGCGCAAAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCttt                                                                 <  2:181863/144‑1 (MQ=255)                                                                                       aacaaGGCAGTCAGAAACATCAAGGTGCCGAAC‑AACATCAACGGCGAAGTCAGACAAATATTACCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGAt                                                      <  1:745698/151‑1 (MQ=255)                                                                                        aaaaggCAGTAACCAAAATCAATGTCCCGGAC‑AACATCACCGGCGAAGCCACACAAATATTACCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATc                                                     <  1:407312/146‑1 (MQ=255)                                                                                               aGTCAGCAACATCAATGTGCCGGAC‑AACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCagc                                              >  2:514324/1‑151 (MQ=255)                                                                                                   agaaaCATAAATGTGCCGGAC‑AACACCAACGGCGAAGCCAGACAAATATTACCCAGCGAATACCCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCagcgagc                                          <  1:145666/148‑1 (MQ=255)                                                                                                            aaTGTGCCGGAC‑AACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATcc                                 >  2:456915/1‑151 (MQ=255)                                                                                                                 tcccggaaacctcaaaCGGGGAAGTCAGACAAATATTACCCGGCGTAAAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCAc                               <  2:541390/135‑1 (MQ=255)                                                                                                                  cgggAC‑AACACCACCGGGGAAGTCAGACAAATTTTACCCCGCGCAAACCCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTg                           <  2:155721/149‑1 (MQ=255)                                                                                                                       aaaacaTCAACGGCGAAGTCAGACAAATATTACCCAGCGCAAAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGAcc                        <  1:648514/148‑1 (MQ=255)                                                                                                                                  ggCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGACCAGCCGACGGGa             >  2:199106/1‑150 (MQ=255)                                                                                                                                  ggCAAAGTAAGCCAAATATTACCCAGCACAAAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGACCAGCCGACggg              <  1:18538/149‑1 (MQ=255)                                                                                                                                     gAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGACCAGCCGACGGGAAcc          >  2:455072/1‑150 (MQ=255)                                                                                                                                      aggtaagcccAATATATCCCAGCCCAAAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGACCAGCCGACGGGAACCaa        <  1:231677/143‑1 (MQ=255)                                                                                                                                      aaGTAAGACAAATATTACCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGACCAGCCGACGGGAACCa         <  1:290292/150‑1 (MQ=255)                                                                                                                                          cAGACTAATATTACCAGGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGACCAGCCGACGGGAACCAATg      <  2:712694/149‑1 (MQ=255)                                                                                                                                            gACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGACCAGCCGACGGGAACCAATGCaa   >  2:697045/1‑150 (MQ=255)                                                                                                                                              ccAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGACCAGCCGACGGGAACCAATGCaaa  >  1:456295/1‑149 (MQ=255)                                                                                                                                                aaTATTACCCAGCGCAAAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGACCAGCCGACGGGAACCAATGCaa   <  2:498129/146‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                            CCGGATATGTAAGAACAGCAACAACTACTGACCAACGCTTCTTTACCTGATATCAGGATTTCTTCATTTTCACCTTTGCAGTAACCAACAATGCAGTCAGCAACATCAATGTGCCGGAC‑AACATCAACGGCGAAGTCAGACCAATATTATCCAGCGCATAACCGCCGATTGCCGCGCCACAGGTATTAGCAAGCTGAATAACCGCCACCTGAATAGACCCGGCTTTTTCTGCCTGATCGGCCAGCGAGCGGGTGATCCACGTTGACCAGCCGACGGGAACCAATGCAAA  >  NC_000913/3840497‑3840785

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑