Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,397,830	0	T	C	46.3%	48.3 / 10.7	42	I265V (ATT→GTT)	uspE	stress‑induced protein
Reads supporting (aligned to +/- strand):  ref base T (18/4);  new base C (0/19);  total (18/24)
Fisher's exact test for biased strand distribution p-value = 5.49e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTCTTCGTCATCCAGTTCAACGGGTGTCTGATACTGGTCAGGTTTAATGACCAGCAGGTCGCAGCGAAGATGATCAATCACCTGTTCCGCCGTGTTGCCGAGGAATGCTGCTGAAATACCGGTGCGTCCTACCGTGCCCAGAACCACAATCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGTTTTCATTAATGCCGAATTTCTGCCGCAGGGCTTTCATTGCCAGCAAATGTTGCCCACGAATGGCATCGTTAT  >  NC_000913/1397681‑1397973                                                                                                                                                      |                                                                                                                                                ttcttcGTCATCCAGTTCAACGGGTGTCTGATACTGGTCAGGTTTAATGACCAGCAGGTCGCAGCGAAGATGATCAATCACCTGTTCCGCCGTGTTGCCGAGGAATGCTGCTGAAATACCGGTGCGTCCTACCGTGCCCAGAACCACAATc                                                                                                                                                >  1:404908/1‑151 (MQ=255)    ttcGTCATCCAGTTCAACGGGTGTCTGATACTGGTCAGGTTTAATGACCAGCAGGTCGCAGCGAAGATGATCAATCACCTGTTCCGCCGTGTTGCCGAGGAATGCTGCTGAAATACCGGTGCGTCCTACCGTGCCCAGAACCACAATcccc                                                                                                                                             >  1:48245/1‑151 (MQ=255)      cGTCATCCAGTTCAACGGGTGTCTGATACTGGTCAGGTTTAATGACCAGCAGGTCGCAGCGAAGATGATCAATCACCTGTTCCGCCGTGTTGCCGAGGAATGCTGCTGAAATACCGGTGCGTCCTACCGTGCCCAGAACCACAATCCCCGc                                                                                                                                           >  2:439574/1‑151 (MQ=255)       gTCATCCAGTTCAACGGGTGTCTGATACTGGTCAGGTTTAATGACCAGCAGGTCGCAGCGAAGATGATCAATCACCTGTTCCGCCGTGTTGCCGAGGAATGCTGCTGAAATACCGGTGCGTCCTACCGTGCCCAGAACCACAATCCCCGcc                                                                                                                                          >  2:19744/1‑151 (MQ=255)                       ggTGTCTGATACTGGTCAGGTTTAATGACCAGCAGGCCGCAGCGAAGATGATCAATCCCCTGTCCCGCCGTGTTGCGGAGGAATGCGGCTGAAATCCCGGTGCGTCCTACGGTGCCCAGACCCAAAACCCCCGCCTGTAAGTGCTCCGCCa                                                                                                                          <  1:668912/151‑1 (MQ=255)                        gtgtTTGATACTGGTCAGGTTTAATGACCAGCGGGTCGCAGCAAAGATGATCAATCCCCTGTCCCGCCGTGTTGCCGAGGAATGCTGCTGAAATACCGGGGCGTCCTACGGTCCCCAAAACCACAACCCCCGCCTGTAAGTGCTCCGc                                                                                                                            <  1:40063/148‑1 (MQ=255)                                 aCTGGTCAGGTTTAATGACCAGCAGGTCGCAGCGAAGATGATCAATCACCTGTTCCGCCGTGTTGCCGAGGAATGCTGCTGAAATCCCGGTGCGTCCTACCGTGCCCAGAACCACAACCCCCGCCTGTAAGTGCTCCGCCAAATCAGGaa                                                                                                                 <  2:179971/150‑1 (MQ=255)                                       cggttttAATGACCAGCAGGTCGCAGCGAAGATGATCAATCCCCTGTCCCGCCGTGTTGCCGAGAAATGCGGCTAAAATCCGGGTGCGTCCTACCGTGCCCAGACCCACAATCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACct                                                                                                           <  2:671620/146‑1 (MQ=255)                                         gtttaaaTGACCAGCGGGTCGCAGCGAAGATGATCAATCCCTTTTCCCGCCGTGTTGCCGAGGAATGCTGCTGAAATCCCGGTGCTTCCTACGGTGCCCAAAACCACAACCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCtctt                                                                                                        <  2:371841/146‑1 (MQ=255)                                            ttAATGACCAGCAGGTCGCAGCGAAGATGATCAATCACCTGTTCCGCCGTGTTGCCGAGGAATGCTGCTGAAATACCGGTGCGTCCTACCGTGCCCAGAACCACAATCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTg                                                                                                     >  2:788563/1‑151 (MQ=255)                                             tAATGACCAGCAGGTCGCAGCGAAGATGATCAATCACCTGTTCCGCCGTGTTGCCGAGGAATGCTGCTGAAATACCGGTGCGTCCTACCGTGCCCAGAACCACAATCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTgg                                                                                                    >  2:756006/1‑151 (MQ=255)                                                   ccaccaGGGCGCAGGGAAGATGAACAATCACCTGTCCCGCCGTGTTCCCGAGGAATGCGGCGGAAATACCGGGGCGTCATACCGTGCCCAGACCCAAACCCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCa                                                                                                  <  1:701401/147‑1 (MQ=255)                                                     agcagGTCGCAGCGAAGATGATCAATCCCCTGTTCCGCCGTGTTGCCGAGGAATGCTGCTGAAATCCCGGTGCGTCCTCCCGTCCCAAGAACCACAATCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCt                                                                                             <  2:165376/150‑1 (MQ=255)                                                                     gagaatcactccCCTGTCCCGCCTTGTTGCCGAGGAATGCTGCAGAAATCCCGGTGCCCCCTACCGCCCCCAGACCCACAACCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTc                                                                              <  1:496444/145‑1 (MQ=255)                                                                        gatCAATCCCCTGTCCCGCCGTGTGGCCGAGGAATGCTGCTAAAATCCCGGTGCGTCCTACCGTGCCCAGACCCACAACCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCa                                                                             <  2:401281/147‑1 (MQ=255)                                                                        gatCAATCACCTGTTCCGCCGTGTTGCCGAGGAATGCTGCTGAAATACCGGTGCGTCCTACCGTGCCCAGAACCACAATCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGtt                                                                         >  2:383371/1‑151 (MQ=255)                                                                            aatccCTTGTCCCGCCGTGTTGCCGAGGATTGCTGCTAAAATCCCGGTGCGTCCTCCCGTCCCCAGACCCACAATCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGttt                                                                        <  2:531781/148‑1 (MQ=255)                                                                            aacccccTGTTCCGCCGTGTTGCCGAGGAATGCTGCTGAAATCCCGGTGCGTCCTACCGTGCCCAGAACCAAAACCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGtttt                                                                       <  2:501054/144‑1 (MQ=255)                                                                                 ccTGTCCCGCCGTGTTGCCGAGGAATGCTGCTGAAATACCGGTGCGTCCTACCGTGCCCAGAACCACAACCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGTTTTCATTAAt                                                                <  2:13041/151‑1 (MQ=255)                                                                                          ccgTGTTGCCGAGGAATGCTGCTGAAATACCGGTGCGTCCTACCGTGCCCAGAACCACAATCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGTTTTCATTAATGCCGAAttt                                                       >  1:64847/1‑151 (MQ=255)                                                                                             tgtTGCCGAGGAATGCTGCTGAAATACCGGTGCGTCCTACGGTGCCCAGAACCACAATCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGTTTTCATTAATGCCGAATTTCTg                                                    >  1:533585/1‑151 (MQ=255)                                                                                              gtTGCCGAGGAATGCTGCTGAAATACCGGTGCGTCCTACCGCGCCCAGAACCACAATCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGTTTTCATTAATGCCGAATTTCTGc                                                   >  1:117700/1‑151 (MQ=255)                                                                                               ttcccGAGAAATGCTGCTGAAATCCCGGTGCGTCCTACCGGCCCCAAACCCACAATCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGTTTTCATTAATGCCGAATTTCt                                                     <  1:3872/145‑1 (MQ=255)                                                                                                    gAGGAATGCTGCTGAAATACCGGTGCGTCCTACCGTGCCCAGAACCACAATCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGTTTTCATTAATGCCGAATTTCTGCCGCAgg                                             >  2:411149/1‑151 (MQ=255)                                                                                                          tgctgcTGAAATACCGGTGCGTCCTACCGTGCCCAGAACCACAATCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGTTTTCATTAATGCCGAATTTCTGCCGCAGGGCTTTc                                       >  1:665389/1‑151 (MQ=255)                                                                                                            ctgcaaaaaTCCCGGGCCGCCCTCCCGCGCCCAGACCCACACCCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGTTTTCATTAATGCCGAATTTCTGCCGCAGGGCTTTc                                       <  1:516551/143‑1 (MQ=255)                                                                                                                tgAATTCCCGGTGCGTCCAACCATCCCCAGAACCACAACCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGTTTTCATTAATGCCGAATTTCTGCCGCAGGGCTTTCa                                      <  1:152075/146‑1 (MQ=255)                                                                                                                tgAAATACCGGTGCGTCCTACCGTGCCCAGAACCACAATCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGTTTTCATTAATGCCGAATTTCTGCCGCAGGGCTTTCATTGcc                                 >  2:579338/1‑151 (MQ=255)                                                                                                                  aaaTCCCGGGCCCTCCAACCGGCCCCAGACCCACAACCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGTTTTCATTAATGCCGAATTTCTGCCGCAGGGCTTTCATTGCCAg                               <  1:725020/151‑1 (MQ=255)                                                                                                                   aaTCCCGGTGCGCCCTACCTTCCCAAGACCCACAACCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGTTTTCATTAATGCCGAATTTCTGCCGCAGGGCTTTCATTGCCAGc                              <  1:756070/151‑1 (MQ=255)                                                                                                                    aaaccgggccccccTACCGTCCCCAAACCCACAACCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGTTTTCATTAATGCCGAATTTCTGCCGCAGGGCTTTCATTGCCAGCa                             <  1:439592/139‑1 (MQ=255)                                                                                                                              gTCCTACCGTGCCCAGAACCACAATCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGTTTTCATTAATGCCGAATTTCTGCCGCAGGGCTTTCATTGCCAGCAAATGTTGccc                   >  2:655030/1‑151 (MQ=255)                                                                                                                                ccTCCCGTCCCCAAAACCACAACCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGTTTTCATTAATGCCGAATTTCTGCCGCAGGGCTTTCATTGCCAGCAAATGTTGCCCAc                 <  2:48243/151‑1 (MQ=255)                                                                                                                                ccTACCGTGCCCAGAACCACAATCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGTTTTCATTAATGCCGAATTTCTGCCGCAGGGCTTTCATTGCCAGCAAATGTTGCCCAc                 >  1:422531/1‑151 (MQ=255)                                                                                                                                 cTACCGTGCCCAGAACCACAATCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGTTTTCATTAATGCCGAATTTCTGCCGCAGGGCTTTCATTGCCAGCAAATGTTGCCCACg                >  1:62015/1‑151 (MQ=255)                                                                                                                                    ccGTGCCAAGACCCACAACCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGTTTTCATTAATGCCGAATTTCTGCCGCAGGGCTTTCATTGCCAGCAAATGTTGCCCa                  <  1:660614/146‑1 (MQ=255)                                                                                                                                         cccAGAACCACAATCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGTTTTCATTAATGCCGAATTTCTGCCGCAGGGCTTTCATTGCCAGCAAATGTTGCCCACGAATGGCAt        >  2:768287/1‑151 (MQ=255)                                                                                                                                         ccaaGAACCACACCCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGTTTTCATTAATGCCGAATTTCTGCCGCAGGGCTTTCATTGCCAGCAAATGTTGCCCACGAATGGCAt        <  1:256920/148‑1 (MQ=255)                                                                                                                                           cAGAACCACAATCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGTTTTCATTAATGCCGAATTTCTGCCGCAGGGCTTTCATTGCCAGCAAATGTTGCCCACGAATGGCATCg      >  2:706432/1‑151 (MQ=255)                                                                                                                                              acccACAACCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGTTTTCATTAATGCCGAATTTCTGCCGCAGGGCTTTCATTGCCAGCAAATGTTGCCCACGAATGGCATCGt     <  2:623137/147‑1 (MQ=255)                                                                                                                                              aaCCACAAGCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGTTTTCATTAATGCCGAATTTCTGCCGCAGGGCTTTCATTGCCAGCAAATGTTGCCCACGAATGGCATc       <  2:309383/147‑1 (MQ=255)                                                                                                                                                ccACAACCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGTTTTCATTAATGCCGAATTTCTGCCGCAGGGCTTTCATTGCCAGCAAATGTTGCCCACGAATGGCATCGTtat  <  1:586977/150‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                TTCTTCGTCATCCAGTTCAACGGGTGTCTGATACTGGTCAGGTTTAATGACCAGCAGGTCGCAGCGAAGATGATCAATCACCTGTTCCGCCGTGTTGCCGAGGAATGCTGCTGAAATACCGGTGCGTCCTACCGTGCCCAGAACCACAATCCCCGCCTGTAAGTGCTCCGCCAAATCAGGAATCACCTCTTCTGGCAGACCTTTTTCTACGTGCGTCATGTTTTCATTAATGCCGAATTTCTGCCGCAGGGCTTTCATTGCCAGCAAATGTTGCCCACGAATGGCATCGTTAT  >  NC_000913/1397681‑1397973

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: ‑