Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,585,078	0	A	C	42.9%	65.7 / 15.9	49	intergenic (+35/+3)	yrhB/ggt	stable heat shock chaperone/gamma‑glutamyltranspeptidase
Reads supporting (aligned to +/- strand):  ref base A (22/6);  new base C (0/21);  total (22/27)
Fisher's exact test for biased strand distribution p-value = 7.74e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CACCTTTTATTATTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAA‑CCGCTGGAAGAA‑TATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTT‑AGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACTTTCTGACCTTTTGCTTCCAGCAGCTTGAGCGT  >  NC_000913/3584928‑3585227                                                                                                                                                         |                                                                                                                                                       cACCTTTTATTATTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAA‑CCGCTGGAAGAA‑TATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTaa                                                                                                                                                        <  2:478416/151‑1 (MQ=255)      tttATTATTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAA‑CCGCTGGAAGAA‑TATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCtt                                                                                                                                                    >  2:404075/1‑150 (MQ=255)       ttattaTTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAA‑CCGCTGGAAGAA‑TATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCtt                                                                                                                                                    >  1:15128/1‑149 (MQ=255)       ttattaTTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAA‑CCGCTGGAAGAA‑TATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTT‑a                                                                                                                                                  <  2:521445/150‑1 (MQ=255)        tattatTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAA‑CCGCTGGAAGAA‑TATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTT‑Ag                                                                                                                                                 <  2:276833/150‑1 (MQ=255)           tattGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAA‑CCGCTGGAAGAA‑TATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTT‑AGTAcc                                                                                                                                             >  2:344739/1‑151 (MQ=255)                   aaGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAA‑CCGCTGGAAGAA‑TATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTT‑AGTACCCCGCCGtt                                                                                                                                     >  2:79569/1‑151 (MQ=255)                       cAGTGGTGAAATTCATTCTCTGGGAACGGCAAAA‑CCGCTGGAAGAA‑TATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTT‑AGTACCCCGCCGTTAAat                                                                                                                                 >  1:36759/1‑151 (MQ=255)                         gtggtaAAATTCATTCTCGGGGAACGGCAAAC‑CCGCTGAAAAAA‑TATCTACAGGATTACAAAAAAAAAAAGGCTCCCTTCGGCTTGCCCTGAAAAAATACCCCTCTCCCCACGAAGAGGGCCGCTAACCTT‑AGTCCCCCGCCGTTAAatc                                                                                                                                <  2:791535/150‑1 (MQ=255)                                    cattcTCTGGGAACGGCAAAA‑CCGTTGGAAGAA‑TATCTACAGGATTACGAAATAAAAAAGGATACCTTCGGCTTGCCCTGACAAAATACCCCTCTTCCCACGAAGAGGGCCGCTAACCTT‑AGTACCCCGCCGTTAAACCATCCACCGAgtg                                                                                                                    >  1:648159/1‑149 (MQ=255)                                     attcTCTGGGAACGGCAAAA‑CCGCTGGAAGAA‑TATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTT‑AGTACCCCGCCGTTAAATCATCCACCGAgcgc                                                                                                                   >  1:983242/1‑151 (MQ=255)                                      ttcCCTGGGAGCGCAAACC‑CCGCGGGAAGAA‑TATCTACAGGCTTACAAAAAAAAAGAGGCTACCTCCGTCTCCCCCTAACAAAATCCCCCTCTCCCCGC‑AAGGGGGCCCGTAAACTTAAGCCCCCCGCCGTTAAATCATCCACCGAgc                                                                                                                     <  1:205738/148‑1 (MQ=255)                                          ctGGGAACGGCAAAA‑CCGCTGGAAGAA‑TATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTT‑AGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTc                                                                                                              >  2:423025/1‑151 (MQ=255)                                           cgggAAAGGAAAAACCCGCGGAAAAAA‑TATCTAAAGAATAAAAAAAAAAAAAAGGCTCCCTTCGGCTTCCCCTAAAAAAATCCCCCTCTCCCCACGAAGAGGCCCGCTACCCTT‑AGTCCCCCGCCGTTAAATCATCCACCGAGCGCggg                                                                                                                <  1:573405/148‑1 (MQ=255)                                            gggAACGGAAAAC‑CCGCTGGAAGAA‑TATCTAAAGGATTAAAAAAAAAAAAAGGCTTCCTCCGGCTTGCCCTGACAAAGTACCCCTCTCCCCCGGAGGGGGCCCGCTACCCTT‑TGTCCCCCGCCGTTAAATCATCCACCGAgcgc                                                                                                                   <  2:154880/144‑1 (MQ=255)                                            gggAACGACAAAC‑CCGCTGAAAGAA‑TATCTACAGGATTACAAAATAAAAAAGGCTCCCTTCGGCTTGCCCTGACAAAATGCCCCTCTTCCCACGAAGGGGCCCGCTACCCTT‑AGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCgg                                                                                                            <  2:901473/151‑1 (MQ=255)                                             gggaaggaaaaa‑CCCGTGGAAAAATTATATACAGGTTAACAAAAAAAAAAGAGCTCCTTTCGCCTTGCCCTAACAAAATCGCCCTCTCCCCGGGAAGAGGGCCGTTACCCTT‑ATACCCCCGCCGTTAAATCATCCACCGAGCGCGGGTc                                                                                                              <  1:1026047/141‑1 (MQ=255)                                                 cgccAAAA‑CCGCGGAAAGAA‑AATCTACAGGATTACAAAAAAAAAAAGGCTCCCTCCGGCTTCCCCTAACAAAATACCCCTCCCCCCCCGAAGGGGGCCGCTACCCTT‑ATTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGa                                                                                                           <  1:781448/144‑1 (MQ=255)                                                 cGGAAAAC‑CCGCTGAAAAAA‑TATCTACAGGATTAAAAAAAAAAAAAGCCTCCCTTCGGCTTCCCCTAAAAAAATACCCCTCTCCCCACGAAGGGGCCCGCTACCCTT‑AGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATgc                                                                                                        <  2:676377/150‑1 (MQ=255)                                                        a‑CCGCTGGAAGAA‑TATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTT‑AGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTAc                                                                                                 >  2:1125968/1‑150 (MQ=255)                                                          ccGCTGGAAGAA‑TATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTT‑AGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACa                                                                                                >  2:335131/1‑150 (MQ=255)                                                                 cagaa‑TATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTACCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTT‑AGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCg                                                                                        >  1:702448/2‑151 (MQ=255)                                                                 aaaaa‑TATCTACAGGATAAAAAAAAAAAAAGGGCTCCCTGCGGCTTCCCCTGAAAAAATACCCCTCCCCCCCGAAAGAGGGCCGCAACCCTT‑AGCCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCa                                                                                           <  1:937674/145‑1 (MQ=255)                                                                 aaaaa‑TATCAACAGAATTAAAAAAAAAAAAGGGCTCCCTCCTGCTTGCCCGGAAAAAATGCCCTTCTCCCCAAGAAGGGGGCCGCTACCTTT‑AGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACa                                                                                                <  1:901229/140‑1 (MQ=255)                                                                  aaaa‑TATCAACAGGTTAACAAAAAAAAAAAGCCTCCCTCCGCCTTCCCCTAAAAAAATCCCCCTCTCCCCACGAGGGGGGCCGTTACCCTT‑AGCCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGt                                                                                       <  1:79546/149‑1 (MQ=255)                                                                    aa‑TATCTACAGGATTACAAAAAAAAAAAGGCTCCCTCCGGCTTCCCCTGACAAAATACCCCTCTCCCCACGAGGAGGGCCGCTACCCTT‑AGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTcc                                                                                     <  2:932724/151‑1 (MQ=255)                                                                       tatCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTT‑AGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCgg                                                                                   >  2:926733/1‑151 (MQ=255)                                                                          cTACAGTATTACGAAAAAAAAAAGGCTCCCTTCGGCTTGCCCTAAAAAAATAGCCCTCTCCCCACGAAGAGGGCCGCTACCCTT‑AGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCg                                                                                    <  2:568320/147‑1 (MQ=255)                                                                          cTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTT‑AGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGccc                                                                                >  2:30149/1‑151 (MQ=255)                                                                           tACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTT‑AGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGccc                                                                                >  1:681382/1‑150 (MQ=255)                                                                                      aaaaaaaaaaaGCCTCCCTTCGGCTTCCCCTAAAAAAATACCCCTCTCCCCACGAAGGGGCCCGCTAACCTT‑AGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCt                                                                    <  1:504519/150‑1 (MQ=255)                                                                                       aaaaaaaaaaGGCTCCCTTCGGCTTCCCCTAAAAAAATACCCTTCTCCCCACGAAGGGGCCCGCTACCCTT‑AGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATa                                                                         <  2:635816/145‑1 (MQ=255)                                                                                            aaaaaGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTT‑AGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTgtgt                                                              >  1:161554/1‑151 (MQ=255)                                                                                                        ttCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTT‑AGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGc                                                  >  1:1029377/1‑151 (MQ=255)                                                                                                                gCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTT‑AGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTc                                           >  1:1188594/1‑150 (MQ=255)                                                                                                                   cTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTT‑AGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAgc                                        >  1:1124977/1‑150 (MQ=255)                                                                                                                   cTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTT‑AGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAgc                                        >  1:529412/1‑150 (MQ=255)                                                                                                                      aaaaaaTAGCCCTCTCCCCACGAAGAGGCCCGCTACCCTT‑AGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGcc                                     <  2:1118832/148‑1 (MQ=255)                                                                                                                        aaaaTCCCCCTCTCCCCACGAAGGGGCCCGCTACCCTT‑AGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACt                                  <  2:137389/151‑1 (MQ=255)                                                                                                                         aaaTAGCCCTCTTCCCACGAGGAGGCCCGCTACCCTA‑AGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACtt                                 <  2:1188858/151‑1 (MQ=255)                                                                                                                          aaTACCCCTCTCCCCACGAAGGGGGCCGCAACCCTT‑AGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACttt                                <  2:102475/151‑1 (MQ=255)                                                                                                                           atcccccTCCCCCCACGAAGAGGGCCGCTACCCTT‑AGCCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACTTTc                               <  1:161513/147‑1 (MQ=255)                                                                                                                             aGCCCTCTTCCCACGAAGAGGGCCGCTAACCTT‑AGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACTTTCt                              >  1:458616/1‑150 (MQ=255)                                                                                                                               cccTCTTCCCACGAAGAGGGCCGCTAACCTT‑AGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACTTTCTGAc                           >  1:375724/1‑151 (MQ=255)                                                                                                                               cccTCTCCCCACGAAGAGGCCCGCTACCCTT‑AGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACTTTCTg                             <  2:1157148/149‑1 (MQ=255)                                                                                                                                     ccccACGAGGGGGCCCCCAAACTTT‑ACTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACTTTCTGACCtttt                      <  1:885455/149‑1 (MQ=255)                                                                                                                                     ccccACGAAGGGGCCCGCTACCCTT‑AGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACTTTCTGACCtt                        <  2:75598/147‑1 (MQ=255)                                                                                                                                      cccACGAAGAGGGCCGCTAACCTT‑AGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACTTTCTGACCTTTTGc                    >  2:765371/1‑151 (MQ=255)                                                                                                                                                    cGCTACCTTT‑AGCCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACTTTCTGACCTTTTGCTTCCAGCAGCTTGa      <  1:1173500/151‑1 (MQ=255)                                                                                                                                                    cGCTACCCTT‑AGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACTTTCTGACCTTTTGCTTCCAGCAGCTTGa      <  2:693301/151‑1 (MQ=255)                                                                                                                                                         aCCTT‑AGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACTTTCTGACCTTTTGCTTCCAGCAGCTTGAGCGt  >  1:242825/1‑150 (MQ=255)                                                                                                                                                         |                                                                                                                                                       CACCTTTTATTATTGATAAAGACAGTGGTGAAATTCATTCTCTGGGAACGGCAAAA‑CCGCTGGAAGAA‑TATCTACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTT‑AGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAATGCTTTGTGTACTGCCCATCGCCTCTTTCAGCGCCACTTTCTGACCTTTTGCTTCCAGCAGCTTGAGCGT  >  NC_000913/3584928‑3585227

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: ‑