Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,001,164	0	A	C	51.2%	32.2 / 66.9	41	T274P (ACC→CCC)	xdhA	xanthine dehydrogenase, molybdenum binding subunit
Reads supporting (aligned to +/- strand):  ref base A (17/3);  new base C (0/21);  total (17/24)
Fisher's exact test for biased strand distribution p-value = 7.52e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.93e-06

TGCGTACGAGTCATCAAACCATTTGTCGGTGGCGGTTTTGGTAATAAACAGGATGTACTGGAAGAGCCAATGGCGGCATTCCTGACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAG‑TTT‑CCC‑TTAGCCGTGAAGAGTGTTT‑CCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACGGGCACTCCATCGCTTCTGCGGGGGGGAATAA  >  NC_000913/3001017‑3001309                                                                                                                                                         |                                                                                                                                                  tGCGTACGAGTCATCAAACCATTTGTCGGTGGCGGTTTTGGTAATAAACAGGATGTACTGGAAGAGCCAATGGCGGCATTCCTGACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAG‑TTT‑CCC‑TTAGCCGTGAAGAGTGTTT‑CCTCGCAAccc                                                                                                                                                >  2:628692/1‑151 (MQ=255)       cGAGTCATCAAACCATTTGTCGGTGGCGGTTTTGGTAATAAACAGGATGTACTGGAAGAGCCAATGGCGGCATTCCTGACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAG‑TTT‑CCC‑TTAGCCGTGAAGAGTGTTT‑CCTCGCAACCCGTAccc                                                                                                                                          <  1:524489/151‑1 (MQ=255)                    cATTTGTCGGTGGCGGTTTTGGTAATAAACAGGATGTACTGGAAGAGCCAATGGCGGCATTCCTGACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAG‑TTT‑CCC‑TTAGCCGTGAAGAGTGTTT‑CCTCGCAACCCGTACCCGCCACGCTTTTAc                                                                                                                             >  2:412352/1‑151 (MQ=255)                      tttGTCGGTGGCGGTTTTGGTAATAAACAGGATGTACTGGAAGAGCCAATGGCGGCATTCCTGACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAG‑TTT‑CCC‑TTAGCCGTGAAGAGTGTTT‑CCTCGCAACCCGTACCCGCCACGCTTTTaac                                                                                                                            >  1:718647/1‑148 (MQ=255)                           cGGTGGCGGTTTTGGTAATAAACAGGATGTACTGGAAGAGCCAATGGCGGCATTCCTGACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAG‑TTT‑CCC‑TTAGCCGTGAAGAGTGTTT‑CCTCGCAACCCGTACCCGCCACGCTTTTACCATTGAc                                                                                                                      >  1:99917/1‑151 (MQ=255)                                    ttttGGTAATAAACAGGATGTACTGGAAGAGCCAATGGCGGCATTCCTGACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAG‑TTT‑CCC‑TTAGCCGTGAAGAGTGTTT‑CCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATg                                                                                                             >  1:276964/1‑151 (MQ=255)                                    tttgGGAAATAACCAGGTTGTACGGAAGGAGCCATGGGCGGCTTCCCTACCCA‑GCAGCCGTGGCGGCATCCCGGAAAACG‑TTC‑CCC‑TTAGCTGGGAAGAGTTTTT‑CCCCCCACCCCGTACCCGCCACGCTTTTACCATTGACGGGCaaa                                                                                                               <  2:134898/149‑1 (MQ=255)                                     tttgaaaaaaaaCGGGATGTACGGAAAGACCAAAGGGCGCCTTTCCCGACCA‑GCAGGCTGGGCGGC‑TTCCGGGGAAAG‑TTT‑CCCTTTAGCCGAAAAGAGTGTTT‑CCCCCCACCCCGTCCCCGCCACGCTTTTACCATTGACGGGCAAATg                                                                                                             <  1:234099/141‑1 (MQ=255)                                        gaaaataaACAGGATTTACGGGAGGACCCAAGGGCGGCTTTCCCGCCCA‑GCAAGCTGGGCGCCATTCCGGTGAAAT‑TTC‑CCC‑TTGGCCGTGAAGAGTGTTC‑CCCCGCCCCCCGTCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGc                                                                                                          <  1:43996/147‑1 (MQ=255)                                           aaaaaaCAGGTTGTACGGAAAGAGCCAATGGCGGCATTCCTCACCA‑GCAGGTTGGGCGGCATCCGGGTAAAAT‑TTT‑CCT‑TTAGCCGTGAAGGGTTTTC‑CCCCGCACCCCGTCCCCGCCACGCTTTTACCATTGACGGGCAAATggg                                                                                                           <  2:147033/143‑1 (MQ=255)                                                aCAGGATGTACTGGAAGAGCCAATGGCGGCATTCCTGACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAG‑TTT‑CCC‑TTAGCCGTGAAGAGTGTTT‑CCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACcgc                                                                                                 >  2:410704/1‑151 (MQ=255)                                                   ggATTTACGGAAAGAGCAAAGGGGGGCTTTCCTGACCA‑GAAAGTTGGGCGGCATTCGGGTGAAAG‑TTC‑CCC‑TTGGCGGTAAAGAGTTTTC‑CCTCCCACCCGGTCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACcgcg                                                                                                <  2:473741/149‑1 (MQ=255)                                                    ggttgtgcggAAGGGGCAAAGGGGGCCTTCCCGGCCCGGCAAGTTGGGCGCCATTCGGGTAAAAT‑TTC‑CCC‑TTGGCCGTAAAGGGTTTTC‑CCCCCCACCCCGTCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACcgcg                                                                                                <  2:314036/141‑1 (MQ=255)                                                      tttACTAGAAGAGCCAATGGCGTCTTTCCTCCCCA‑ACACGCTTGGCGCCTTTCCGGTAAATG‑TTC‑CCC‑TTCGCCGTGAAGATTTTTT‑CCCCCCACCCCTTCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACgg                                                                                            <  2:2870/148‑1 (MQ=255)                                                      tGTACTGGAAGAGCCAATGGCGGCATTCCTGACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAG‑TTT‑CCC‑TTAGCCGTGAAGAGTGTTT‑CCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACgg                                                                                            >  2:293712/1‑150 (MQ=255)                                                        tgcggaaggagCCAGGGGCGCCTTCCCGGCCCA‑GC‑AGGTTGGGGGGCTTCCGGGTAAAT‑TTTCCCC‑TTAGCGGGGAGGGTTTTTC‑CCCCGCCCCCCGTCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACg                                                                                             <  1:166776/139‑1 (MQ=255)                                                              aaGAGCCAGGGGGCGCATTCCAGCCCA‑GAAAGCTGGGCGCCATCCCGG‑GAAAGTTTT‑CCT‑TTAACCGTGAAGGGTGTTC‑TCCCGAACCCCGTCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGaa                                                                                   <  1:193587/151‑1 (MQ=255)                                                              aaGAGCAAAGGGCGGCTTCCCTGCCCA‑GCAAGCTGGGCGGCTTCCGGGTAAAAT‑TTC‑CCC‑TGGGCCGGGAAGAGTTTTC‑CCCCGCACCCCGTCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGa                                                                                    <  2:113681/150‑1 (MQ=255)                                                                gagCCAATGGCGGCATTCCTGACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAG‑TTT‑CCC‑TTAGCCGTGAAGAGTGTTT‑CCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGaa                                                                                   >  2:240577/1‑149 (MQ=255)                                                                     aggggcgccATTCCTAACCA‑GCAAGCTGGGCGCCATCCGGGAAAAAT‑TTC‑CCC‑TTGGCGGTGAAGGGTTTTC‑CCCCCCACCCCTTCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGaaa                                                                                  <  2:276980/142‑1 (MQ=255)                                                                          cggcATTCCTGACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAG‑TTT‑CCC‑TTAGCCGTGAAGAGTGTTT‑CCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCt                                                                       >  2:782729/1‑151 (MQ=255)                                                                          cggcATTCCTGACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAG‑TTT‑CCC‑TTAGCCGTGAAGAGTGTTT‑CCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCt                                                                       >  2:204571/1‑151 (MQ=255)                                                                           gtcttcccTCACCA‑GCAGGTTTGTCGGCTTTCGGTTAAAAT‑TTC‑CCC‑TAATCCGGAAAGATTGTTC‑CCTGAATACCCTTCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTc                                                                        <  1:762594/143‑1 (MQ=255)                                                                           ggcATTCCTGCCCA‑GAAGGCTGGCCGTCTGTCGGGTAATCG‑TTC‑CCC‑TTACCGGGGAGGTTTTTTC‑CCCCCCTACCCGCCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTc                                                                        <  1:188089/149‑1 (MQ=255)                                                                           ggcATCCCTGCCCA‑GCAGGCGTGGCGGCTTTCGGGT‑AAAT‑TTT‑CCC‑CTTGGCGGGAAAGGTTTTTCCCCCCCCCCCCGTCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTg                                                                      <  1:707486/151‑1 (MQ=255)                                                                                            aggCTGGGCGGCATCCCGGGAAAAT‑TTC‑CCC‑TTAGCGGTGAAGGGTGTTC‑CCCCCCCCCCCTTCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCt                                                          <  2:825639/145‑1 (MQ=255)                                                                                            aagttggggggcATTCGGTTAAAAT‑TTC‑CCC‑TTGGCGGAAAAGGGTTTTC‑CCCCCCCCCCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGt                                                            <  1:412323/136‑1 (MQ=255)                                                                                              gCTTGGCGGCATTCCGGTGAAAG‑TTT‑CCC‑TTAGCCGTGAAGAGTGTTT‑CCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACAcc                                                    >  2:327745/1‑151 (MQ=255)                                                                                                   gcgccgttCCGGTGAAAT‑TTC‑CCC‑TTAGCCGTGAGGGGTTTTT‑CCTCGCCCCCCGTCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCgg                                                  <  1:5377/142‑1 (MQ=255)                                                                                                    cggcATTCCGGTGAAAG‑TTT‑CCC‑TTAGCCGTGAAGAGTGTTT‑CCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCt                                              >  1:302711/1‑151 (MQ=255)                                                                                                      ccgttCCGGTAAATT‑TTT‑CCC‑TTAGCCGTGAGGTTTTTTT‑CCCCGCACCCCGTCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGgcgc                                               <  2:235122/145‑1 (MQ=255)                                                                                                         ttCCGGTGAAAG‑TTT‑CCC‑TTAGCCGTGAAGAGTGTTT‑CCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGc                                         >  2:827003/1‑151 (MQ=255)                                                                                                             ggagAAAT‑TTC‑CCC‑TTAGCGGTAAAGGTTTTCC‑CCTCGCCCCCCGCCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCAtct                                     <  1:55344/148‑1 (MQ=255)                                                                                                              gggAAAT‑TTT‑CCCTTTGGCGGTGATGAGTTTTT‑CCCCGCCCCCCATCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGc                                         <  2:262197/145‑1 (MQ=255)                                                                                                                  aagtttt‑CCC‑TTGGCCGTGAAGGTTTTTT‑CCCCGCACCCCGTCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCAt                                       <  1:301878/141‑1 (MQ=255)                                                                                                                                   cGTGAAGAGTGTTT‑CCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACGGGCACTCCATCGCtt                  >  2:673006/1‑151 (MQ=255)                                                                                                                                        ccgttttttcccccGCACCCCGTCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACGGGCACTCCATCGCTTCt                <  1:640159/136‑1 (MQ=255)                                                                                                                                            tgtTT‑CCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAAGATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACGGGCACTCCATCGCTTCTGCgggg          >  2:503926/1‑150 (MQ=255)                                                                                                                                              ttt‑CCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACGGGCACTCCATCGCTTCt                >  2:640200/1‑142 (MQ=255)                                                                                                                                                  ccccGCACCCCGTCCCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACGGGCACTCCATCGCTTCTGCggggggg       <  2:318746/145‑1 (MQ=255)                                                                                                                                                     cGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACGGGCACTCCATCGCTTCTGCGGGGGGGAATaa  >  1:492042/1‑150 (MQ=255)                                                                                                                                                         |                                                                                                                                                  TGCGTACGAGTCATCAAACCATTTGTCGGTGGCGGTTTTGGTAATAAACAGGATGTACTGGAAGAGCCAATGGCGGCATTCCTGACCA‑GCAAGCTTGGCGGCATTCCGGTGAAAG‑TTT‑CCC‑TTAGCCGTGAAGAGTGTTT‑CCTCGCAACCCGTACCCGCCACGCTTTTACCATTGACGGGCAAATGGGCGTGAACCGCGACGGAACATTGAAAGGTTATAGTCTGGATGTTCTGTCTAACACCGGCGCTTATGCATCTCACGGGCACTCCATCGCTTCTGCGGGGGGGAATAA  >  NC_000913/3001017‑3001309

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑