Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,364,396	0	A	T	40.0%	78.0 / 21.8	50	P530P (CCA→CCT)	yhcD	putative outer membrane fimbrial subunit usher protein
Reads supporting (aligned to +/- strand):  ref base A (24/6);  new base T (0/20);  total (24/26)
Fisher's exact test for biased strand distribution p-value = 5.11e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACAATGACTCAAGCAACCTTAATATTAACTGGAACAAAGCGTTCAAACACGCCACGGTTTCCGTCAACTGGCAGCATCAACTTAGTGCTTCAGAAAATAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCAGATGAGATGTCCTACTATGTGAATGCTGAACGAGATCACGACGAACGTGAAACGAGCT  >  NC_000913/3364254‑3364541                                                                                                                                               |                                                                                                                                                  aCAATGACTCAAGCAACCTTAATATTAACTGGAACAAAGCGTTCAAACACGCCACGGTTTCCGTCAACTGGCAGCATCAACTTAGTGCTTCAGAAAATAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGc                                                                                                                                             >  1:679170/1‑149 (MQ=255)      caCTCAAGCAACCTTAATATTAACTGGAACAAAGCGTGCAAACACGCCACGGTTTCCGTCAACTGGCAGCATCAACTTAGTGCTTCAGACAATAATGAAGACGATGGTGTTCTGTTCTACGTCAACATCAGCATTCGATTTGGCAGATCa                                                                                                                                       >  2:460946/2‑150 (MQ=255)          cAAGCAACCTTAATATTAACTGGAACAAAGCGTTCAAACACGCCACGGTTTCCGTCAACTGGCAGCATCAACTTAGTGCTTCAGAAAATAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAaca                                                                                                                                   <  2:327976/150‑1 (MQ=255)                 ccTTAATATTAACTGGAACAAAGCGTTCAAACACGCCACGGTTTCCGTCAACTGGCAGCATCAACTTAGTGCTTCAGAAAATAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCcac                                                                                                                            >  1:40311/1‑150 (MQ=255)                  cTTAATATTAACTGGAACAAAGCGTTCAAACACGCCACGGTTTCCGTCAACTGGCAGCATCAACTTAGTGCTTCAGAAAATAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCacac                                                                                                                          >  2:397963/1‑151 (MQ=255)                    tAATATTAACTGGAACAAAGCGTTCAAACACGCCACGGTTTCCGTCAACTGGCAGCATCAACTTAGTGCTTCAGAAAATAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTg                                                                                                                        >  1:572518/1‑151 (MQ=255)                     aaTATTAACGGAAACAAAGCGTTAAAACACGCCACGGTTTCCGTAAACGGGCAGCATCAACTTAGTGCTTCAAAAAATAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCTTTTGGCAGATCAAACACCGCCACACt                                                                                                                         <  1:194763/149‑1 (MQ=255)                           aaCTGGAACAAAGCTTTAAACCACGCCCCGTTTTCCGTCAACTGGCAGCATCAATTTAGTGTTTCAGAAAATAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCTTTTGGCAGATAAAACACCGCCACACTGTATACTc                                                                                                                 <  1:76179/151‑1 (MQ=255)                              tGGAACAAAGCGTTCAAACACGCCACGGTTTCCGTCAACTGGCAGCATCAACTTAGTGCTTCAGAAAATAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGcc                                                                                                              >  2:61392/1‑151 (MQ=255)                               ggAACAAAGCTTTAAAACACGCCACGGTTTCCGTCAACTGGCAGCATCAACTTAGTGCTTCAAAAAATAATGAAGACGTTGGTGATCTGTTCTCCGTCAACATCAGTATTCCTTTTGGCAGATCAAACACCGCCACACTGTATACTCGcc                                                                                                              <  1:598813/150‑1 (MQ=255)                                 aaCAAAGCGTTCAAACACGCCACGGTTTCCGTCAACTGGCAGCATCAACTTAGTGCTTCAGAAAATAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATg                                                                                                           >  1:142504/1‑151 (MQ=255)                                    aaaGCGTTCAAACACGCCACGGTTTCCGTCAACTGGCAGCATCAACTTAGTGCTTCAGAAAATAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACAGCCACACTGTATACTCGCCATGACg                                                                                                        >  2:106506/1‑151 (MQ=255)                                          ttaaaaCACGCCACGTTTTCCGTCAACTGGCAGCATCAACTTAGTGCTTCAAAAAATAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCTTTTGGCAGATAAAACACCGCCACACTGTATACTCGCCATGACGATc                                                                                                     <  1:331171/145‑1 (MQ=255)                                           tCAAACACGCCACGGTTTCCGTCAACTGGCAGCATCAACTTAGTGCTTCAGAAAATAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATa                                                                                                  >  2:70201/1‑150 (MQ=255)                                              accacGCCACGTTTCCCTTCAACTGGCAGCATAAACTTAGTGCTTAAGAAAATAATAAAAACGAGGGTAATTTGTTTTACGTCAACATCAGTATCCTTTTTGGCAGAAAAAACACCGCCACACTGTATACTCGCCATGACGATCATaa                                                                                                 <  2:103160/146‑1 (MQ=255)                                                      acgttgtcggTCAACTGGCAGCATCAATTTAGTGCTTCAGAAAATAATGAATACGATGGTAATCTGTTCTACTTAAACATAATTATTCTATTTGGCAGATCAACCACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTAt                                                                                       <  2:38847/141‑1 (MQ=255)                                                         gTTTCCGTCAACTGGCAGCATCAACTTAGTGCTTCAGAAAATAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGt                                                                                    >  1:697828/1‑150 (MQ=255)                                                                      ggagccttCAATTTAGTGCTACAAAAAAAAATAAAGCGTATGGTGTTCTTTTCTCCGTCAACATCATTTTCCCATTTGGCAGATCAACCACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATgg                                                                       <  2:910157/143‑1 (MQ=255)                                                                      ggaagtataaaCTTGGGGCTTCAGAAAATAATGAACAGGTGGGTTTTTTTTTTTCCGTCAAAATAGGTATTCATTTGGGCGGATAAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCAt                                                                         <  2:795037/139‑1 (MQ=255)                                                                             tCAACTTAGTGTTTAAAAAAAAAAGAAAGACGTTGGTGTTCTGTTCTACGACAACACAATTATTCCATTTAGAAGATAAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAgtc                                                                  <  2:407188/148‑1 (MQ=255)                                                                              cattttAGTGCTACAAAAAATAATGAAGACGATGTTGATCTGTTCTCCCTCAACATCAGTATTCCTTTTGGCAGATCAACCACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAgtc                                                                  <  1:136827/143‑1 (MQ=255)                                                                               accTTATTGCTTAAAAAAAAAAGGAAGACGTTGTTGTTCTTTTCTCCGTCAACATCAGTATTCCTTTTGGCAGTTCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAgtcg                                                                 <  1:543599/145‑1 (MQ=255)                                                                               aaCTTAGTGCTTCAGAAAATAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGAGAGTCGtctc                                                             >  1:143967/1‑151 (MQ=255)                                                                                  ttAGTGCTTCAGAAAATAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGtctc                                                             >  1:45896/1‑148 (MQ=255)                                                                                  ttAGTGCTTCAGAAAATAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGtctc                                                             >  2:814433/1‑148 (MQ=255)                                                                                  ttAGTGCTTCAAAAAATAAGGAAGACGATGGTGATCTGTTCTCCGTAAACATCAGTTTTCCTTTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCa                                                            <  1:77796/149‑1 (MQ=255)                                                                                   tAGTGCTTCAGAAAATAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGtctc                                                             >  2:966148/1‑147 (MQ=255)                                                                                   tAGTGCTTCAAAAAATAATGAAGACGATGGTGATCTGTTCTCCGTCAACATCATTATTCCTTTTGGCAGATCAACCACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCa                                                            <  1:167654/148‑1 (MQ=255)                                                                                          taaaaaaaTAATAAAGACGTTGGTTTTCTGTTCTACGTCAACATCATTATTCCTTTTGGCAAAACAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCagatgagatg                                                   <  1:658502/146‑1 (MQ=255)                                                                                              aaaaTAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCTTTTGGCAGATAAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCAGATGAGATGTCcta                                              <  1:441182/151‑1 (MQ=255)                                                                                               aaaTAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCAGATGAGATGTCctac                                             >  1:456814/1‑151 (MQ=255)                                                                                                   aaggAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCTTTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCAGATGAGATGTCCTACTAt                                          <  1:832318/147‑1 (MQ=255)                                                                                                      gAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCAGATGAGATGTCCTACTAtgtg                                       >  2:389640/1‑150 (MQ=255)                                                                                                      gAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCAGATGAGATGTCCTACTAtgtg                                       >  1:325941/1‑150 (MQ=255)                                                                                                       aaGACGGTGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAACCACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCAGATGAGATGTCCTACTATGTGa                                      <  1:296711/150‑1 (MQ=255)                                                                                                        aGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCAGATGAGATGTCCTACTATGTGAAt                                    >  1:429677/1‑151 (MQ=255)                                                                                                        aGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCAGATGAGATGTCCTACTATGTGAAt                                    >  2:693045/1‑151 (MQ=255)                                                                                                          aCGATGGTGATCTGTTCTACGTCAACATCATTATTCCTTTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCAGATGAGATGTCCTACTATGTGAATg                                   <  2:631144/150‑1 (MQ=255)                                                                                                           cGATGGTGATCTTTTTTCCGTCAACATCAGTATTCCTTTTGGCAGACCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCAGATGAGATGTCCTACTATGTGAATGc                                  <  1:404984/150‑1 (MQ=255)                                                                                                            gacggTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCAGATGAGATGTCCTACTATGTGAATg                                   >  2:374418/4‑148 (MQ=255)                                                                                                            gATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCAGATGAGATGTCCTACTATGTGAATGCTg                                >  1:970014/1‑151 (MQ=255)                                                                                                             cgctcttccattcttACGTCAACATCAGTATCCCTTTGGGAAAATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCAGATGAGATGTCCTACTATGTGAATGCTg                                <  2:449401/136‑1 (MQ=255)                                                                                                              tGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCAGATGAGATGTCCTACTATGTGAATGCTGa                               >  2:291618/1‑150 (MQ=255)                                                                                                                    tCTTTTCTCCGCCAAAATCATTATTCCATTTGCAAGAACAACCACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCAGATGAGATGTCCTACTATGTGAATGCTGAACga                           <  2:528941/148‑1 (MQ=255)                                                                                                                      tttccTACGTAACCATCATTGTTCCTTTTGGCAAATCAACCGCCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCAGATGAGATGTCCTACTATGTGAATGCTGa                               <  2:642239/138‑1 (MQ=255)                                                                                                                        ttCTACGTAAACATCAGTATTCCTTTTGGCAGACCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCAGATGAGATGTCCTACTATGTGAATGCTGAACGAGATCa                      <  2:572377/149‑1 (MQ=255)                                                                                                                           tACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCAGATGAGATGTCCTACTATGTGAATGCTg                                >  1:449518/1‑136 (MQ=255)                                                                                                                              gtaaaCATCATTATTCCTTTTGGCAAATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCAGATGAGATGTCCTACTATGTGAATGCTGAACGAGATCacgac                  <  2:870982/144‑1 (MQ=255)                                                                                                                                  aCATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCAGATGAGATGTCCTACTATGTGAATGCTGAACGAGATCACGACGAACGTg           >  2:659204/1‑150 (MQ=255)                                                                                                                                           ttCCTTTTGGCAGATAAAACTCCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCAGATGAGATGTCCTACTATGTGAATGCTGAACGAGATCACGACGAACGTGAAACGAGCt  <  1:535962/150‑1 (MQ=255)                                                                                                                                               |                                                                                                                                                  ACAATGACTCAAGCAACCTTAATATTAACTGGAACAAAGCGTTCAAACACGCCACGGTTTCCGTCAACTGGCAGCATCAACTTAGTGCTTCAGAAAATAATGAAGACGATGGTGATCTGTTCTACGTCAACATCAGTATTCCATTTGGCAGATCAAACACCGCCACACTGTATACTCGCCATGACGATCATAAAACCCACTATGGTACTGGTGTCATGGGAGTCGTCTCAGATGAGATGTCCTACTATGTGAATGCTGAACGAGATCACGACGAACGTGAAACGAGCT  >  NC_000913/3364254‑3364541

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑