Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	15,395	0	G	A	45.8%	46.1 / 25.3	48	intergenic (+97/‑50)	dnaJ/insL1	chaperone Hsp40, DnaK co‑chaperone/IS186 transposase
Reads supporting (aligned to +/- strand):  ref base G (4/22);  new base A (22/0);  total (26/22)
Fisher's exact test for biased strand distribution p-value = 5.67e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAAAGAGCTTCTTTGATGGTGTGAAGAAGTTTTTTGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATG‑AATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGCTCT  >  NC_000913/15246‑15536                                                                                                                                                      |                                                                                                                                               cAAAGAGCTTCTTTGATGGTGTGAAGAAGTTTTTTGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAgc                                                                                                                                               <  2:501693/151‑1 (MQ=255)    agagCTTCTTTGATGGTGTGAAGAAGTTTTTTGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCt                                                                                                                                            <  2:304494/151‑1 (MQ=255)          tcttTGATGGTGTGAAGAAGTTTTTTGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACt                                                                                                                                        <  2:533600/149‑1 (MQ=255)                  ggTGTGAAGAAGTTTTTTGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTtg                                                                                                                               <  2:72946/150‑1 (MQ=255)                   gtgtGAAGAAGTTTTTTGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTtgtg                                                                                                                             <  2:342764/151‑1 (MQ=255)                      tgAAGAAGTTTTTTGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGGCACCCCCACAAACGCTAACTTAAggggt                                                                                                                                >  1:1021992/1‑143 (MQ=255)                       gaagaaGTTTTTTGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGGGACTCCCCTAAACCGTAACTTAAAGGGTGTgg                                                                                                                            >  1:223575/1‑148 (MQ=255)                            agTTTTTTGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTAACTTCCCTAAAGGCTCACCTTATGGTTGTgggaggt                                                                                                                       >  1:911881/1‑143 (MQ=255)                             gTTTTTTGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGcc                                                                                                                   <  1:353788/151‑1 (MQ=255)                                       gacCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGGCACTCCCCTAAACGCTAAATTTAGGGGTGTGGGATTATGCCTGGTATGAtt                                                                                                         >  1:903949/1‑151 (MQ=255)                                               ccGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTCACCCCCCTAAGCGGTAAATTAAGGGGTTTGGGATTTCGCCTGttaatgttttacat                                                                                                   >  2:569882/1‑138 (MQ=255)                                                 gCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCg                                                                                               <  1:947674/151‑1 (MQ=255)                                                    aaCCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATg                                                                                            <  1:500000/151‑1 (MQ=255)                                                             aaaaGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATG‑AATTActct                                                                                  <  1:440070/151‑1 (MQ=255)                                                              aaaGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATG‑AATTACtctc                                                                                 <  1:216064/151‑1 (MQ=255)                                                                aGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTCAATCCCATAAACGCTAAATTAAAGGGTGTGGGGTTATGCCTGATATTATTTTAAGTGCCGATG‑AATTACtctccc                                                                               >  2:41106/1‑149 (MQ=255)                                                                     gtccGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATG‑AATTACTCTCACGATaa                                                                          <  2:672490/149‑1 (MQ=255)                                                                         gTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTCACTCCCCTAAACGCCCACTTAAAGGGTGTGGGATTTCGCCCGGTATGATTTTAAGTGCCGGTG‑AATTAATCTCCCGaaaa                                                                          >  2:1041973/1‑147 (MQ=255)                                                                              cAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGGTACTCCCCCAAACGCCTACTTTAAGGGTGGGGGATTTCGCCTGATATGATTTTAAGTGCCGGAG‑AAATAATCTCACGaaaaataggt                                                                    >  1:1047011/1‑142 (MQ=255)                                                                               aGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATG‑AATTACTCTCACGATAACTGGTCAGCa                                                                <  2:651967/151‑1 (MQ=255)                                                                                  ccTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTTACACCCCCAAATGCTAAATTTAGGGGTGGGGGATATCGCCTGGTTTGTTTTTAATTGCCGATG‑AATTATTTTCACCATAACTTGTGAGCAAtt                                                             >  1:817952/1‑151 (MQ=255)                                                                                  ccTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTCACTCCCATAAACGCTAACTTAAGGGGTGTGGGATTTAGCCTGATATGATTTTAAGTGCCGATG‑AATTACTTTCCCGATAACTGGGCAGCAAtt                                                             >  2:456299/1‑151 (MQ=255)                                                                                    tGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAACGCCAACTTAAAGGGTGTGGGGTTACGCCTGATATTATTTTAAGTGCCGATG‑AATTACTCTCACGATAACTGGTCAGCAAATCt                                                           >  2:766160/1‑151 (MQ=21)                                                                                     gggTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATG‑AATTACTCTCACGATAACTGGTCAGCAATTCTg                                                          <  1:251979/151‑1 (MQ=255)                                                                                      ggTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTCACCCCCCTAAACGCCAACTTTAGGGGTGTGGGTTTTTGCCTGATATGATTTTACGTGCCGGTG‑AAATACTCTCACGATAAATGGTGAGCAAATCt                                                           >  2:58758/1‑149 (MQ=255)                                                                                       gTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATG‑AATTACTCTCACGATAACTGGTCAGCAATTCTGGc                                                        <  2:946638/151‑1 (MQ=255)                                                                                         aaaaaTAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGAGAACACCCCCCTAAACGCCAAATTAAAGGGTGGGGGATTATGGCTGGTATGATTTTACGTGGCGGTGAAATTATTTTC‑CCATAAACTGTCAGCAAATCTTGccc                                                      >  1:421515/1‑151 (MQ=255)                                                                                          aaaaTAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATG‑AATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCa                                                     <  1:458862/151‑1 (MQ=255)                                                                                           aaaTAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATG‑AATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCat                                                    <  2:1017719/151‑1 (MQ=255)                                                                                             aTAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTCACTCCCCTAAACGCTCACTTTAGGGGTGTGGTATTACGCCTGGTATGATTTTACGTGGCGATG‑AATTAATCTCCCGATAAATGGTCAGCAAATCTTGccc                                                      >  2:179610/1‑147 (MQ=255)                                                                                                   tGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTCACTCCCATAAACGCTAACTTAAGGGGTGTGGGATTACGCCTGATATGATTTTAAGTGCCGATG‑AATTAATCTCACGATAAATGGTCAGCAATTCTTGCCCATATTgg                                               >  2:351909/1‑148 (MQ=255)                                                                                                      gTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGACACTCCCCCAAACGCCAACTTTAGGGGTGTGGGATTTAGCCTGATATGATTTTAACTGCCCATG‑AATTAATCTCCCGCTAAATGGGCAGGAATTCTTGCCCCTATTTGTaaagc                                         >  2:601377/1‑148 (MQ=255)                                                                                                         gAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATG‑AATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCga                                      <  1:606155/151‑1 (MQ=255)                                                                                                          aaGATATGCGAGCACCTGTAAAGTGGCGGGGGACACCCCCCTAAACGCCAACTTAAGGGGTGTGGGATTACGCCCGGTATGATTTTAAGTGGCGCTG‑AATTATTCTCCCCAGAAATGGTCAGCAAATTTTGCCCACAtttggaaaacc                                        >  1:388862/1‑139 (MQ=255)                                                                                                          aaGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATG‑AATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCgaa                                     <  1:764985/151‑1 (MQ=255)                                                                                                           aGATATGCGAGCACCTGTAAAGTGGCGGGGATCACCCCCATAAACGCACACAAACAGGGTGTGGTGATACCCCTCATATTACTTTAGGTGCCGAAT‑AATTAACCCCCCTAGAAATGGTCAGCAATCTTGGccccaatttgggtgccc                                        >  2:693566/1‑133 (MQ=255)                                                                                                             atatGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATG‑AATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCgaagaa                                  <  1:94378/151‑1 (MQ=255)                                                                                                              tatGCGAGCACCTGTAAAGTGGCGGGGGACACCCCCCTAAACGCTAACCTAAAGGGTGTGGGATTATGCCTGATATGATTTTATGTGCCGGTG‑AATTACTCTCACGATAAATGGTCAGCAATTCTCGGCCCTAtt                                                 >  1:282805/1‑135 (MQ=255)                                                                                                                 gCGAGCACCTGTAAAGTGGCGGGGGTCACTCCCCTAAACGCTAACTTAAAGGGTGTGGGATTAAGCCTGGTATGATTTTAAGGGCCGATG‑AAATAATCTCACGATAAATGGTCAGCAAATCTGGCCCCTATTTGTAAACCCGAAGAACAgg                              >  2:238438/1‑151 (MQ=255)                                                                                                                    aGCACCTGTAAAGTGGCGGGGAACACTCCCATAAACGCTCAAATAAAGGGTGTGGGATTTCGCCCGGTATTATTTTACGTGCCGATG‑GAATACTCCCCCCCTAAACGGGCAGCAAATTTTGCCCCTATTTGTAAACCCgaagaaaagg                              >  1:549324/1‑144 (MQ=255)                                                                                                                     gCACCTGTAAAGTGGCGGGGGTCACTCCCCTCAACCCCAACTTTAAGGGTGTGGGATTTCGCCTGATATGATTTTAAGTGGCGATG‑AAATATTCTCACGATAACTTGGTAGCCAATCTTGCCCCTAATTGTAAAGCCgaagaaatcg                              >  1:631851/1‑143 (MQ=255)                                                                                                                           gTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATG‑AATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGc                    <  1:999765/151‑1 (MQ=40)                                                                                                                              aaGTGGCGGGGATCACTCCCCTAAACGCTAACTTTAGGGGTGTGGTATTACGCCTGATATGATTTAACGTGCCGATG‑AATTACTCTCACGATAAATGGTCAGCAATTTTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGccc                  >  1:803827/1‑148 (MQ=14)                                                                                                                              aaGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATG‑AATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACg                 <  1:32221/151‑1 (MQ=38)                                                                                                                                gTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATG‑AATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTa               <  2:593459/151‑1 (MQ=37)                                                                                                                                   gCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATG‑AATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTaa              <  1:544523/149‑1 (MQ=34)                                                                                                                                    cGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATG‑AATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGc           >  2:246302/1‑151 (MQ=33)                                                                                                                                           cACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATG‑AATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGct    >  1:252918/1‑151 (MQ=31)                                                                                                                                             cTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATG‑AATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGctct  >  1:255420/1‑151 (MQ=11)                                                                                                                                                      |                                                                                                                                               CAAAGAGCTTCTTTGATGGTGTGAAGAAGTTTTTTGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATG‑AATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGCTCT  >  NC_000913/15246‑15536

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑